Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo-0.70.0.dist-info/METADATA @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 Metadata-Version: 2.1
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2 Name: planemo
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3 Version: 0.70.0
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4 Summary: Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
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5 Home-page: https://github.com/galaxyproject/planemo
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6 Author: Galaxy Project and Community
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7 Author-email: jmchilton@gmail.com
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8 License: AFL
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9 Keywords: planemo
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10 Platform: UNKNOWN
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11 Classifier: Development Status :: 5 - Production/Stable
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12 Classifier: Intended Audience :: Developers
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13 Classifier: Environment :: Console
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14 Classifier: License :: OSI Approved :: Academic Free License (AFL)
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15 Classifier: Operating System :: POSIX
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16 Classifier: Topic :: Software Development
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17 Classifier: Topic :: Software Development :: Code Generators
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18 Classifier: Topic :: Software Development :: Testing
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19 Classifier: Natural Language :: English
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20 Classifier: Programming Language :: Python :: 2
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21 Classifier: Programming Language :: Python :: 2.7
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22 Classifier: Programming Language :: Python :: 3
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23 Classifier: Programming Language :: Python :: 3.5
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24 Classifier: Programming Language :: Python :: 3.6
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25 Classifier: Programming Language :: Python :: 3.7
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26 Classifier: Programming Language :: Python :: 3.8
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27 Description-Content-Type: text/x-rst
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28 Requires-Dist: aenum
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29 Requires-Dist: BeautifulSoup4
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30 Requires-Dist: bioblend (>=0.13.0)
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31 Requires-Dist: Click
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32 Requires-Dist: configparser
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33 Requires-Dist: cwltool (==1.0.20191225192155)
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34 Requires-Dist: docutils
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35 Requires-Dist: ephemeris (>=0.10.3)
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36 Requires-Dist: galaxy-containers
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37 Requires-Dist: galaxy-tool-util (>=20.1.0.dev2)
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38 Requires-Dist: galaxy-util (>=20.1.0.dev0)
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39 Requires-Dist: glob2
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40 Requires-Dist: gxformat2 (>=0.8.0)
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41 Requires-Dist: jinja2
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42 Requires-Dist: lxml
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43 Requires-Dist: oyaml
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44 Requires-Dist: pyaml
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45 Requires-Dist: pyyaml
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46 Requires-Dist: six (>=1.7.0)
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47 Requires-Dist: virtualenv
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48
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49 .. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png
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50 :alt: Planemo Logo
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51 :align: center
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52 :figwidth: 100%
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53 :target: https://github.com/galaxyproject/planemo
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54
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55 Command-line utilities to assist in developing Galaxy_ and `Common Workflow Language`_ tools.
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56
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57 .. image:: https://readthedocs.org/projects/planemo/badge/?version=latest
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58 :target: http://planemo.readthedocs.io/en/latest/?badge=latest
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59 :alt: Documentation Status
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60
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61 .. image:: https://badge.fury.io/py/planemo.svg
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62 :target: https://pypi.python.org/pypi/planemo/
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63 :alt: Planemo on the Python Package Index (PyPI)
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64
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65 .. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master
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66 :target: https://travis-ci.org/galaxyproject/planemo
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67 :alt: Build Status
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68
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69 .. image:: https://travis-ci.org/jmchilton/planemo-extended-tests.svg?branch=master
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70 :target: https://travis-ci.org/jmchilton/planemo-extended-tests
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71 :alt: Build Status of Extended Tests
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72
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73 .. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master
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74 :target: https://coveralls.io/r/galaxyproject/planemo?branch=master
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75 :alt: Coverage Status
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76
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77 * Free software: Academic Free License version 3.0
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78 * Documentation: https://planemo.readthedocs.io.
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79 * Code: https://github.com/galaxyproject/planemo
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80
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81
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82 Quick Start
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83 -----------
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84
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85 -----------------
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86 Obtaining
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87 -----------------
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88
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89 For a traditional Python installation of Planemo, first set up a virtualenv
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90 for ``planemo`` (this example creates a new one in ``.venv``) and then
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91 install with ``pip``. Planemo requires pip 7.0 or newer.
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92
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93 ::
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94
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95 $ virtualenv .venv; . .venv/bin/activate
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96 $ pip install "pip>=7" # Upgrade pip if needed.
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97 $ pip install planemo
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98
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99 For information on updating Planemo, installing the latest development release,
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100 or installing Planemo via `Bioconda <https://github.com/bioconda/bioconda-recipes>`__
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101 - checkout the `installation <http://planemo.readthedocs.io/en/latest/installation.html>`__
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102 documentation.
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103
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104 Planemo is also available as a `virtual appliance
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105 <https://planemo.readthedocs.io/en/latest/appliance.html>`_ bundled
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106 with a preconfigured Galaxy server and set up for Galaxy_ and
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107 `Common Workflow Language`_ tool development.
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108 You can choose from open virtualization format (OVA_, .ova) or Docker_
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109 appliances.
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110
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111 -----------------
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112 Basics - Galaxy
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113 -----------------
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114
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115 This quick start will assume you have a directory with one or more Galaxy
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116 tool XML files. If no such directory is available, one can be quickly created for
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117 demonstrating ``planemo`` as follows ``project_init --template=demo mytools; cd mytools``.
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118
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119 Planemo can check tool XML files for common problems and best
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120 practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
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121 (also aliased as ``l``).
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122
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123 ::
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124
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125 $ planemo lint
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126
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127 Like many ``planemo`` commands - by default this will search the
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128 current directory and use all tool files it finds. It can be explicitly
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129 passed a path to tool files or a directory of tool files.
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130
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131 ::
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132
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133 $ planemo l randomlines.xml
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134
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135 The ``lint`` command takes in additional options related to
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136 reporting levels, exit code, etc. These options are described
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137 in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
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138 or (like with all commands) can be accessed by passing ``--help`` to it.
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139
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140 ::
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141
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142 $ planemo l --help
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143 Usage: planemo lint [OPTIONS] TOOL_PATH
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144
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145 Once tools are syntactically correct - it is time to test. The ``test``
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146 `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
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147 can be used to test a tool or a directory of tools.
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148
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149 ::
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150
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151 $ planemo test --galaxy_root=../galaxy randomlines.xml
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152
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153 If no ``--galaxy_root`` is defined, Planemo will download and configure
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154 a disposable Galaxy instance for testing.
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155
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156 Planemo will create a HTML output report in the current directory named
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157 ``tool_test_output.html`` (override with ``--test_output``). See an
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158 `example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_
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159 of such a report for Tophat.
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160
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161 Once tools have been linted and tested - the tools can be viewed in a
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162 Galaxy interface using the ``serve`` (``s``) `command
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163 <http://planemo.readthedocs.org/en/latest/commands.html#serve-command>`__.
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164
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165 ::
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166
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167 $ planemo serve
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168
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169 Like ``test``, ``serve`` requires a Galaxy root and one can be
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170 explicitly specified with ``--galaxy_root`` or installed dynamically
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171 with ``--install_galaxy``.
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172
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173 For more information on building Galaxy tools in general please check out
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174 `Building Galaxy Tools Using Planemo`_.
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175
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176 ----------------------------------
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177 Basics - Common Workflow Language
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178 ----------------------------------
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179
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180 This quick start will assume you have a directory with one or more `Common Workflow
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181 Language`_ YAML files. If no such directory is available, one can be quickly created for
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182 demonstrating ``planemo`` as follows ``planemo project_init --template=seqtk_complete_cwl mytools; cd mytools``.
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183
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184 Planemo can check tools YAML files for common problems and best
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185 practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
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186 (also aliased as ``l``).
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187
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188 ::
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189
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190 $ planemo lint
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191
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192 Like many ``planemo`` commands - by default this will search the
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193 current directory and use all tool files it finds. It can be explicitly
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194 passed a path to tool files or a directory of tool files.
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195
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196 ::
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197
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198 $ planemo l seqtk_seq.cwl
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199
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200 The ``lint`` command takes in additional options related to
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201 reporting levels, exit code, etc. These options are described
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202 in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
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203 or (like with all commands) can be accessed by passing ``--help`` to it.
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204
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205 ::
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206
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207 $ planemo l --help
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208 Usage: planemo lint [OPTIONS] TOOL_PATH
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209
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210 Once tools are syntactically correct - it is time to test. The ``test``
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211 `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
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212 can be used to test a CWL tool, workflow, or a directories thereof.
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213
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214 ::
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215
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216 $ planemo test --engine cwltool seqtk_seq.cwl
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217
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218 Planemo will create a HTML output report in the current directory named
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219 ``tool_test_output.html``. Check out the file ``seqtk_seq_tests.yml`` for
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220 an example of Planemo test for a CWL tool. A test consists of any number of
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221 jobs (with input descriptions) and corresponding output assertions.
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222
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223 Checkout the `Commmon Workflow User Guide`_ for more information on developing
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224 CWL tools in general and `Building Common Workflow Language Tools`_ for more
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225 information on using Planemo to develop CWL tools.
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226
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227 ---------
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228 Tool Shed
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229 ---------
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230
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231 Planemo can help you publish tools to the Galaxy Tool Shed.
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232 Check out `Publishing to the Tool Shed`_ for more information.
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233
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234 ------
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235 Conda
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236 ------
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237
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238 Planemo can help develop tools and Conda packages in unison.
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239 Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>`__ or `CWL
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240 <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>`__ version of the "Dependencies and Conda" tutorial
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241 for more information.
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242
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243 -----------------------
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244 Docker and Containers
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245 -----------------------
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246
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247 Planemo can help develop tools that run in "Best Practice" containers for
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248 scientific workflows. Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>`__ or `CWL
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249 <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>`__ version of the "Dependencies and Containers" tutorial for more information.
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250
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251 .. _Galaxy: http://galaxyproject.org/
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252 .. _GitHub: https://github.com/
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253 .. _Conda: http://conda.pydata.org/
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254 .. _Docker: https://www.docker.com/
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255 .. _Vagrant: https://www.vagrantup.com/
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256 .. _Travis CI: http://travis-ci.org/
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257 .. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
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258 .. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
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259 .. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html
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260 .. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
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261 .. _Common Workflow Language: https://www.commonwl.org/
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262 .. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/
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263 .. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html
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264 .. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format
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265
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266
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267
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268
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269
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270 History
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271 -------
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272
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273 .. to_doc
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274
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275 ---------------------
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276 0.70.0 (2020-01-29)
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277 ---------------------
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278
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279 * Temporarily add galaxy-util requirement `Pull Request 991`_
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280 * Make symlinks in tool tree work for planemo test `Pull Request 988`_
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281 * Reduce use of ``shell=True`` in subprocesses `Pull Request 989`_
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282 * Drop planemo database seed option `Pull Request 985`_
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283 * Don't execute ``untar_to()`` subprocesses through the shell `Pull Request 984`_
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284 * Allow setting database_connection for planemo test runs `Pull Request 986`_
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285 * Fix copy-paste mistakes `Pull Request 983`_
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286 * Add planemo list_repos command `Pull Request 982`_
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287 * Make container_register build files with headers and include base_image `Pull Request 980`_
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288 * Replace deprecated galaxy-lib requirement with galaxy-tool-util `Pull Request 978`_
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289 * Close all opened files (thanks to `@bernt-matthias`_). `Pull Request 979`_
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290 * Build single requirement container, log if requirement not in best-practice channels `Pull Request 977`_
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291 * Use tojson jinja2 filter instead of json.dumps `Pull Request 975`_
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292 * Add merge_test_reports command `Pull Request 974`_
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293 * Implement github workflow and fix profile commands if psql unavailable `Pull Request 976`_
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294 * Fix planemo lint --biocontainers if no build number in container `Pull Request 972`_
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295 * Update a training command (thanks to `@hexylena`_). `Pull Request 973`_
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296 * Allow passing through GALAXY_VIRTUAL_ENV variable to venv setup `Pull Request 971`_
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297 * Correct help text (thanks to `@hexylena`_). `Pull Request 970`_
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298 * Remove unneeded html5lib requirement `Pull Request 968`_
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299
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300 ---------------------
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301 0.62.1 (2019-10-14)
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302 ---------------------
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303
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304 * Init & update submodules when installing and creating packages. Stop
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305 distributing eggs (thanks to `@nsoranzo`_). 1ab8530_
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306
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307 ---------------------
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308 0.62.0 (2019-10-11)
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309 ---------------------
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310
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311 * Use ``unicodify()`` on exceptions and subprocess outputs (thanks to
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312 `@nsoranzo`_) `Pull Request 944`_
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313 * Do not override ``None`` with empty string (thanks to `@ic4f`_). `Pull Request
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314 950`_
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315 * Update Docker template for training material generation (thanks to
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316 `@bedroesb`_). `Pull Request 958`_
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317 * Add support for suite of repos with different owners (thanks to `@nsoranzo`_).
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318 `Pull Request 959`_
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319 * Link for collection details updated in the docs (thanks to `@martin-raden`_).
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320 `Pull Request 963`_
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321 * Move most tests to Python 3.7, drop Python 3.4 (thanks to `@nsoranzo`_).
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322 `Pull Request 964`_
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323 * Remove confusing warning `Pull Request 966`_
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324
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325 ---------------------
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326 0.61.0 (2019-07-08)
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327 ---------------------
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328
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329 * Training - fix empty repeat + some formatting (thanks to `@bebatut`_). `Pull
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330 Request 926`_
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331 * Training - add bibliography to tutorial template (thanks to `@shiltemann`_).
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332 `Pull Request 938`_
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333 * Training - support new class definition for input in workflow step (thanks to
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334 `@bebatut`_). `Pull Request 943`_
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335 * Various tool tutorial fixes ahead of GCC 2019 (thanks to `@nsoranzo`_).
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336 `Pull Request 940`_
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337 * Return validation error if doi is empty (thanks to `@nsoranzo`_).
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338 `Pull Request 937`_
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339
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340 ---------------------
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341 0.60.0 (2019-05-31)
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342 ---------------------
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343
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344 * Return validation error if doi is empty `Pull Request 937`_
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345 * Add junit as test reporter (thanks to `@selten`_). `Pull Request 935`_
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346 * Update galaxy.xsd for new python 3 compatibility attribute (thanks to `@martenson`_). `Pull Request
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347 931`_
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348 * Documentation: add a little warning for <param ... multiple="true"> (thanks to
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349 `@bernt-matthias`_). `Pull Request 930`_
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350
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351 ---------------------
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352 0.59.0 (2019-05-09)
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353 ---------------------
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354
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355 * Add ability to test data manager tools (thanks to `@mvdbeek`_).
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356 `Pull Request 912`_
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357 * Update Training for new requirement definition (thanks to `@bebatut`_).
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358 `Pull Request 913`_
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359 * Drop amqp workaround (thanks to `@mvdbeek`_). `Pull Request 917`_
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360 * Use ``yaml.safe_load()`` instead of deprecated ``load()`` (thanks to `@nsoranzo`_).
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361 `Pull Request 921`_
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362 * Allow converting ``tool_test_report.json`` to xunit (thanks to `@mvdbeek`_).
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363 `Pull Request 918`_
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364 * Fix error if testcase.data.job does not exist (thanks to `@mvdbeek`_).
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365 `Pull Request 924`_
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366 * Fix deprecated ``getchildren()`` (thanks to `@nsoranzo`_).
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367 `Pull Request 925`_
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368
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369 ---------------------
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370 0.58.2 (2019-03-01)
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371 ---------------------
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372
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373 * Fix display of tool ids in planemo html report (thanks to `@mvdbeek`_).
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374 `Pull Request 908`_
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375 * Single quotes for file names (thanks to `@bernt-matthias`_). `Pull Request
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376 909`_
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377 * Fix doc linting (thanks to `@mvdbeek`_). `Pull Request 910`_
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378 * Update TS categories (thanks to `@nsoranzo`_). 07dc6e0_
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379 * Close tag in doc help, to help with copy&paste (thanks to `@blankenberg`_).
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380 `Pull Request 914`_
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381 * Update the tool XSD file (thanks to `@bgruening`_). `Pull Request 915`_
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382
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383 ---------------------
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384 0.58.1 (2019-01-03)
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385 ---------------------
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386
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387 * Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to
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388 `@nsoranzo`_). `Pull Request 906`_
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389 * Fix command run by `planemo test --skip_venv` (thanks to `@nsoranzo`_).
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390 `Pull Request 907`_
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391
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392 ---------------------
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393 0.58.0 (2019-01-01)
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394 ---------------------
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395
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396 * Remove deprecated ``sudo: false`` from .travis.yml (thanks to `@nsoranzo`_).
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397 `Pull Request 902`_
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398 * Do not skip Galaxy client build for ``planemo serve``. Install Galaxy when the
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399 directory specified with ``--galaxy_root`` does not exist or is empty. (thanks
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400 to `@nsoranzo`_). `Pull Request 895`_, `Issue 845`_
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401
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402 ---------------------
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403 0.57.1 (2018-11-23)
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404 ---------------------
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405
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406 * Fix username validation for shed linting (thanks to `@martenson`_).
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407 `Pull Request 899`_, `Issue 898`_
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408
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409 ---------------------
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410 0.57.0 (2018-11-19)
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411 ---------------------
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412
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413 * Allow ``workflow_convert`` to convert a native ``.ga`` workflows to format 2 (yaml).
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414 `Pull Request 896`_
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415 * New command (``workflow_edit``) to open workflow in a synchronized graphical editor.
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416 `Pull Request 894`_
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417 * Conda tutorial fixes (thanks to `@nsoranzo`_). `Pull Request 876`_
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418 * Enable ``--conda_use_local`` option for ``planemo test`` (thanks to
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419 `@nsoranzo`_). `Pull Request 876`_
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420 * When testing, skip workflow outputs that do not have a `label` set (thanks to
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421 `@bgruening`_). `Pull Request 893`_
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422 * Add ``__repr__`` for ``TestCase`` to improve debugging Planemo
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423 (thanks to `@bgruening`_). `Pull Request 892`_
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424 * Increase IO polling interval over time (thanks to `@martenson`_).
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425 `Pull Request 891`_
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426 * Sync galaxy xsd and fix tests (thanks to `@mvdbeek`_).
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427 `Pull Request 889`_
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428 * Linting fix for ``W605`` (thanks to `@martenson`_). `Pull Request 888`_
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429 * Add icon for repeat parameters in training (thanks to `@bebatut`_).
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430 `Pull Request 887`_
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431
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432 ---------------------
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433 0.56.0 (2018-10-30)
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434 ---------------------
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435
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436 * Allow selection of Python version when starting managed Galaxy
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437 (thanks to `@mvdbeek`_). `Pull Request 874`_
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438 * Change the channel priority of conda (again). (thanks to `@bgruening`_).
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439 `Pull Request 867`_
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440 * Some small english corrections (thanks to `@hexylena`_). `Pull Request 868`_
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441 * Print the list of excluded paths when running ``ci_find_repos``
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442 (thanks to `@nsoranzo`_). `Pull Request 877`_
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443 * Improved XSD lint reporting. `Pull Request 871`_
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444 * Fix Planemo writing a file called ``gx_venv_None``. `Pull Request 870`_
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445 * Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to
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446 `@nsoranzo`_). `Pull Request 864`_
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447 * Fix to make workflow testing more robust.
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448 `Pull Request 882`_
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449
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450 ---------------------
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451 0.55.0 (2018-09-12)
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452 ---------------------
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453
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454 * Add commands to create Galaxy training materials (thanks to `@bebatut`_).
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455 `Pull Request 861`_
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456 * Fix `planemo test` when TEMP env variable contain spaces (thanks to
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457 `@nsoranzo`_).
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458 `Pull Request 851`_
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459 * Support testing a completely remote galaxy instance (thanks to `@hexylena`_).
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diff changeset
460 `Pull Request 856`_
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461 * Allow naming history from command line (thanks to `@hexylena`_).
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462 `Pull Request 860`_
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463 * Sync galaxy.xsd from galaxy repo (thanks to `@nsoranzo`_).
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464 `Pull Request 866`_
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465 * Fix ServeTestCase.test_shed_serve test (thanks to `@nsoranzo`). bad810a_
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466
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467 ---------------------
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468 0.54.0 (2018-06-06)
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469 ---------------------
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470
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471 * Better support for testings against different versions of Galaxy efficiently and robustly.
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472 `Pull Request 849`_
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473 * New database version (thanks to `@bgruening`_).
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474 `Pull Request 847`_
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475 * Hyperlink DOIs against preferred resolver (thanks to `@katrinleinweber`_).
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476 `Pull Request 850`_
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477 * Tests for collection inputs to workflows. `Pull Request 843`_
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478 * Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust.
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479 b12b117_
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480 * More tutorial testing, tutorial updates.
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481 016b923_, 324c776_, 2002b49_
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482 * More isolated ``test_shed_upload.py`` tests. 72d2ca7_
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483 * Add filetype support for workflow test inputs (thanks to `@bgruening`_).
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484 `Pull Request 842`_
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485 * Add ``--no_shed_install`` option, to prevent shed installs as part of workflow testing.
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486 `Pull Request 841`_
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487 * Small docs fix (thanks to `@hexylena`_). `Pull Request 848`_
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488
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489 ---------------------
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490 0.53.0 (2018-05-22)
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491 ---------------------
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492
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diff changeset
493 * Make Planemo testing easier for CWL tools and workflows in various ways and update
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494 tutorials to reflect these simplifications. `Pull Request 837`_
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diff changeset
495 * Test and fix running workflow tests against externally managed Galaxy servers.
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diff changeset
496 `Pull Request 833`_, `Pull Request 836`_
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diff changeset
497 * Allow using URIs for inputs of workflow test. `Pull Request 840`_
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diff changeset
498 * Slide Galaxy testing window to include 18.05 and drop 17.09. `Pull Request 838`_
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499
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500 ---------------------
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diff changeset
501 0.52.0 (2018-05-20)
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502 ---------------------
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503
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diff changeset
504 * Allow optional disabling of Galaxy single user mode. `Pull Request 835`_
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diff changeset
505 * Fix for path pasting options during workflow testing. `Pull Request 834`_
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506
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507 ---------------------
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diff changeset
508 0.51.0 (2018-05-19)
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509 ---------------------
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diff changeset
510
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diff changeset
511 * Fix essentially all Conda_ and BioContainers_ related functionality to allow parity between
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diff changeset
512 CWL_ and existing Galaxy functionality - fixes and enhances many commands including ``lint``,
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diff changeset
513 ``conda_install``, ``conda_env``, ``test``, ``run``, and ``mull``.
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diff changeset
514 `Pull Request 828`_
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diff changeset
515 * Add two new tutorials for `Conda
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516 <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>`__
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517 and `Container
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518 <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>`__
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diff changeset
519 development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new
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diff changeset
520 CWL exercises, answers, and example project templates.
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diff changeset
521 347c622_
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diff changeset
522 * Improve the CWL generated by the ``tool_init`` command to properly deal with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
523 ``SoftwareRequirement`` s and generate more idiomatic CWL.
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diff changeset
524 `Pull Request 820`_, a5c72e3_
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diff changeset
525 * Add new engine type (``--engine toil``) for testing and running CWL_ tools (requires
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diff changeset
526 manually installing Toil_ with ``pip install toil`` in Planemo's environment).
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diff changeset
527 `Pull Request 831`_
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diff changeset
528 * Add `documentation <http://planemo.readthedocs.io/en/latest/test_format.html>`__
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diff changeset
529 for the Galaxy Workflow and CWL_ test format files (includes information on configuring
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diff changeset
530 various test engines).
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diff changeset
531 `Pull Request 832`_
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diff changeset
532 * Better default logging config for CWL development. `Pull Request 830`_
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533 * Various fixes for the ``conda_search`` command. `Pull Request 826`_
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534 * Fix test coverage configuration. `Pull Request 822`_
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diff changeset
535 * Reorganize .travis.yml for clarity. `Pull Request 829`_
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diff changeset
536 * More isolated, robust unit tests that use git_.
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diff changeset
537 `Pull Request 827`_, `Pull Request 818`_
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538 * Fix default list of best-practice Conda channels. `Pull Request 825`_
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diff changeset
539 * Refactor tests to speed up quick tests - fewer buggy URLs fetched in "quick" mode.
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diff changeset
540 `Pull Request 823`_
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diff changeset
541 * Fix upload configuration of workflow testing to default (overrideable) external Galaxies
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542 to not use path pasting.
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diff changeset
543 `Pull Request 816`_
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diff changeset
544 * Fix test number parsing for workflow tests. `Pull Request 817`_
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diff changeset
545
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diff changeset
546 ---------------------
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diff changeset
547 0.50.1 (2018-05-11)
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diff changeset
548 ---------------------
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diff changeset
549
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diff changeset
550 * Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container ``--engine``.
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diff changeset
551
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diff changeset
552 ---------------------
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diff changeset
553 0.50.0 (2018-05-10)
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diff changeset
554 ---------------------
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diff changeset
555
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diff changeset
556 * Fixes and small CLI tweaks to get the Docker Galaxy container working as an ``--engine`` for the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
557 run, serve, and test commands.
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diff changeset
558
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559 ---------------------
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diff changeset
560 0.49.2 (2018-05-09)
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diff changeset
561 ---------------------
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diff changeset
562
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diff changeset
563 * Various small fixes for new external Galaxy engine type.
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diff changeset
564
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565 ---------------------
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diff changeset
566 0.49.1 (2018-05-06)
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diff changeset
567 ---------------------
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diff changeset
568
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diff changeset
569 * Fix PyPI_ README rendering for 0.49.0 release changes.
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diff changeset
570
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diff changeset
571 ---------------------
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diff changeset
572 0.49.0 (2018-05-06)
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573 ---------------------
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diff changeset
574
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diff changeset
575 * Implement external Galaxy engine. `Pull Request 781`_
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diff changeset
576 * Restructure serve testing code for reuse. `Pull Request 795`_
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diff changeset
577 * Improve test report handling for JSON generated via galaxy-lib testing
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578 script. `Pull Request 799`_
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diff changeset
579 * Improve how various branches of Galaxy are tested. `Pull Request 800`_
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580 * Added documentation for ``GALAXY_MEMORY_MB`` (thanks to `@bernt-matthias`_).
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diff changeset
581 `Pull Request 801`_
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diff changeset
582 * Log tool config in verbose logging mode. `Pull Request 802`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
583 * Replace ``r`` channel with ``conda-forge`` (thanks to `@bgruening`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
584 `Pull Request 805`_
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diff changeset
585 * Sync ``galaxy.xsd`` with latest Galaxy updates (thanks to `@nsoranzo`_).
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diff changeset
586 `Pull Request 806`_
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diff changeset
587 * Use ``requests.get()`` when validating http URLs (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
588 `Pull Request 809`_
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diff changeset
589 * Do not consider tools with "deprecated" in the path (thanks to
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diff changeset
590 `@bgruening`_). `Pull Request 810`_
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diff changeset
591 * Automatically load tools shipped with Galaxy when testing, running, or serving
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592 workflows that reference these tools. `Pull Request 790`_
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593 * Revise README and touch up documentation in general. `Pull Request 787`_
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594 * Various small changes to testing and test framework. `Pull Request 792`_
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595 * Various Python 3 fixes. 8cfe9e9_, 41f7df1_
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596 * Fixes for Galaxy 18.0X releases.
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diff changeset
597 `Pull Request 803`_, dc443d6_
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598
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599 ---------------------
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diff changeset
600 0.48.0 (2018-02-28)
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601 ---------------------
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diff changeset
602
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diff changeset
603 * Run all CI tests against Python 3 (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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604 `Pull Request 768`_ and `Pull Request 774`_
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diff changeset
605 * Python 3 fix - subprocess with ``universal_newlines=True``
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606 (thanks to `@peterjc`_).
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diff changeset
607 `Pull Request 764`_
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diff changeset
608 * Record CWL_ conformance test results using JUnit xml
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diff changeset
609 (thanks to `@mr-c`_).
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diff changeset
610 `Pull Request 756`_
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diff changeset
611 * Restore run test case for simple Galaxy tools.
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diff changeset
612 `Pull Request 769`_
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613 * Enhancements to Galaxy profiles and workflow testing.
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diff changeset
614 `Pull Request 773`_
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615 * Fix resolving & installing shed repositories from workflows for ``test``
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616 and ``run`` commands.
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diff changeset
617 `Pull Request 776`_
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diff changeset
618 * Implement planemo command to convert format 2 workflows into .ga workflows.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
619 `Pull Request 771`_
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diff changeset
620 * Add a native Galaxy workflow (.ga) testing test.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
621 `Pull Request 770`_
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diff changeset
622 * Drop Brew support but add more detailed install instructions.
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diff changeset
623 `Pull Request 761`_
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diff changeset
624 * Clean up CWL_ conformance test execution. `Pull Request 753`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
625 * Assorted small CWL_ and deamon serve fixes. `Pull Request 759`_
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626
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627
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628 ---------------------
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629 0.47.0 (2017-11-18)
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630 ---------------------
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631
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632 * Update to the latest Galaxy tool XSD (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
633 `Pull Request 747`_
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diff changeset
634 * Re-fix problem when shed_update would fail if nothing to update
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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635 (thanks to `@nsoranzo`_). `Pull Request 747`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
636 * Update instructions for installation via conda (thanks to `@nsoranzo`_) .
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
637 `Pull Request 743`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
638 * Bug fix for MacOS `chmod` doesn't support `--recursive` flag.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
639 (thanks to `@dfornika`_). `Pull Request 739`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
640 * Bug fix to also `socket.error` when linting URLs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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641 (thanks to `@nsoranzo`_). `Pull Request 738`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
642 * Disable broken tests. `Pull Request 745`_
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diff changeset
643
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644 ---------------------
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diff changeset
645 0.46.1 (2017-09-26)
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diff changeset
646 ---------------------
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diff changeset
647
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diff changeset
648 * Rev to latest versions of bioblend_ and `galaxy-lib`_ for various fixes
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diff changeset
649 related to CWL_.
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650
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651 ---------------------
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diff changeset
652 0.46.0 (2017-09-15)
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diff changeset
653 ---------------------
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diff changeset
654
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
655 * Change behavior of ``--docker`` flag, for a few releases it would require
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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656 Galaxy use a container for every non-upload tool. This breaks various
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
657 conversion tools for instance and so was reverted.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
658 `Pull Request 733`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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659 * Add 'Accept' header when linting doc URLs (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
660 `Pull Request 725`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
661 * Fix `--conda_auto_install` help (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
662 `Pull Request 727`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
663 * Incremental progress toward CWL support via Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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664 `Pull Request 729`_, `Pull Request 732`_
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665 * Update galaxy-lib to latest version to fix various issues.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
666 `Pull Request 730`_
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diff changeset
667 * Fix lint detected problems with documentation.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
668 `Pull Request 731`_
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diff changeset
669
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670 ---------------------
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diff changeset
671 0.45.0 (2017-09-06)
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672 ---------------------
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673
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diff changeset
674 * Update to the latest `galaxy-lib`_ for Conda fixes. (thanks `@nsoranzo`_)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
675 and updated CWL_ utilities. `Pull Request 716`_, `Pull Request 723`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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676 * Update Conda_ channel order to sync with Bioconda_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
677 (thanks to `@nsoranzo`_). `Pull Request 715`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
678 * Experimental support running CWL_ workflows through the CWL_ fork of Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
679 * Mention ``planemo command --help`` in main help
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
680 (thanks to `@peterjc`_). `Pull Request 709`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
681 * Bugfix handle ``None`` requirement versions when registering containers
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
682 (thanks to `@bgruening`_). `Pull Request 704`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
683 * Bugfix for dependencies by pinning ruamel.yaml version
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
684 (thanks to `@mvdbeek`_). `Pull Request 720`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
685
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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686 ---------------------
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diff changeset
687 0.44.0 (2017-06-22)
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diff changeset
688 ---------------------
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diff changeset
689
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
690 * Fix and improve Galaxy root option specification options.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
691 `Pull Request 701`_, 8a608e0_
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diff changeset
692 * Update `planemo mull` to use a default action of `build-and-test` since
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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693 `build` no longer cleans up itself. ecc1bc2_
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diff changeset
694 * Add a command to pre-install Involucro_.
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diff changeset
695 `Pull Request 702`_
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diff changeset
696
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697 ---------------------
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diff changeset
698 0.43.0 (2017-06-22)
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diff changeset
699 ---------------------
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diff changeset
700
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
701 * Remove stdio from generated tools - just use exit_code for everything.
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diff changeset
702 91b6fa0_
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diff changeset
703 * Implement some ad-hoc documentation tests. `Pull Request 699`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
704 * A large number of small enhancements and fixes for the documentation and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
705 example projects.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
706
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
707 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
708 0.42.1 (2017-06-16)
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parents:
diff changeset
709 ---------------------
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diff changeset
710
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
711 * Fix Readme typos (thanks to `@manabuishii`_) 904d77a_
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712 * Fix `container_register` to create pull requests against the newly finalized home of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
713 multi-package-containers registry repository.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
714 9636682_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
715 * Fix `use_global_config` and `use_env_var` for options with unspecified defaults.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
716 475104c_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
717
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
718
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
719 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
720 0.42.0 (2017-06-15)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
721 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
722
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
723 * Conda/Container documentation and option naming improvements. `Pull Request
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
724 684`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
725 * Sync `galaxy.xsd` with latest upstream Galaxy updates (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
726 `Pull Request 687`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
727 * Fix `ci_find_repos` command to not filter repos whose only modifications where
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
728 in subdirs (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
729 `Pull Request 688`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
730 * Update `container_register` for mulled version 2 and repository name changes.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
731 `Pull Request 689`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
732 * Better pull request messages for the `container_register` command.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
733 `Pull Request 690`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
734
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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735 ---------------------
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diff changeset
736 0.41.0 (2017-06-05)
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737 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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738
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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739 * Fix ``shed_update`` not fail if there is nothing to update
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
740 (thanks to `@nsoranzo`_). `Issue 494`_, `Pull Request 680`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
741 * Conda documentation and option naming improvements.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
742 `Pull Request 683`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
743 * Implement ``container_register`` for tool repositories.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
744 `Pull Request 675`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
745 * Fix ``hub`` binary installation for Mac OS X.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
746 `Pull Request 682`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
747
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
748 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
749 0.40.1 (2017-05-03)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
750 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
751
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
752 * Fix data manager configuration to not conflict with original Galaxy at
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
753 ``galaxy_root`` (thanks to `@nsoranzo`_). `Pull Request 662`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
754 * Fix ``filter_paths()`` to not partial match paths when filtering shed repositories
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
755 (thanks to `@nsoranzo`_). `Pull Request 665`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
756 * Fix description when creating ``.shed.yml`` files (thanks to `@RJMW`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
757 `Pull Request 664`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
758
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
759 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
760 0.40.0 (2017-03-16)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
761 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
762
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
763 * Implement instructions and project template for GA4GH Tool Execution
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
764 Challenge Phase 1. 84c4a73_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
765 * Eliminate Conda hack forcing ``/tmp`` as temp directory. b4ae44d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
766 * Run dependency script tests in isolated directories. 32f41c9_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
767 * Fix OS X bug in ``planemo run`` by reworking it to wait using urllib instead of sockets.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
768 3129216_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
769
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
770 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
771 0.39.0 (2017-03-15)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
772 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
773
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
774 * Implement documentation and examples for Conda-based dependency development (under
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
775 "Advanced" topics).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
776 `Pull Request 642`_, `Pull Request 643`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
777 * Implement documentation and examples for container-based dependency development (under
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
778 "Advanced" topics).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
779 0a1abfe_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
780 * Implement a ``planemo conda_search`` command for searching best practice channels
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
781 from the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
782 `Pull Request 642`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
783 * Allow Planemo to work with locally built Conda packages using the ``--conda_use_local``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
784 command.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
785 `Pull Request 643`_, `Issue 620`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
786 * Implement an ``open`` (or just ``o``) command to quickly open the last test results
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
787 (or any file if supplied). `Pull Request 641`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
788 * Linting improvements and fixes due to `galaxy-lib`_ update.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
789 * WARN on test output names not found or not matching.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
790 * INFO correct information about stdio if profile version is found.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
791 * WARN if profile version is incorrect.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
792 * INFO profile version
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
793 * Fix ``assert_command`` not detected as a valid test (fixes `Issue 260`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
794 * Have ``lint --conda_requirements`` check that at least one actual requirement is found.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
795 6638caa_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
796 * Allow ``conda_install`` to work with packages as well as just tools.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
797 8faf661_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
798 * Add ``--global`` option to conda_install to install requirements into global Conda setup
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
799 instead of using an environment.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
800 8faf661_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
801 * Implement ``planemo lint --biocontainer`` that checks that a tool has an available BioContainer
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
802 registered.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
803 0a1abfe_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
804 * Add more options and more documentation to the ``planemo mull`` command.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
805 0a1abfe_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
806 * Hack around a bug in Conda 4.2 that makes it so ``planemo mull`` doesn't work out of the box on
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
807 Mac OS X.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
808 0a1abfe_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
809 * Allow URIs to be used instead of paths for a couple operations. ce0dc4e_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
810 * Implement non-strict CWL parsing option. 4c0f100_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
811 * Fixes for changes to cwltool_ and general CWL-relate functionality.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
812 3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
813 * Eliminate deprecated XML-based abstraction from ``planemo.tools``. 04238d3_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
814 * Fix ``MANIFEST.in`` entry that was migrated to galaxy-lib. ced5ce2_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
815 * Various fixes for the command ``conda_env``. `Pull Request 640`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
816 * Improved command help - both formatting and content. `Pull Request 639`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
817 * Implement a ``--no_dependency_resolution`` option disabling conda dependency
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
818 resolver.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
819 `Pull Request 635`_, `Issue 633`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
820 * Tests for new linting logic. `Pull Request 638`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
821 * Fix bug where tool IDs needs to be lowercase for the shed (thanks to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
822 `@bgruening`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
823 `Pull Request 649`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
824 * Update seqtk version targetted by intro docs. e343b67_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
825 * Various other Conda usability improvements. `Pull Request 634`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
826
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
827 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
828 0.38.1 (2017-02-06)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
829 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
830
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
831 * Fix bug with ``shed_lint --urls`` introduced in 0.38.0.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
832 84ebc1f_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
833
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
834 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
835 0.38.0 (2017-02-06)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
836 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
837
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
838 * Trim down the default amount of logging during testing.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
839 `Pull Request 629`_, `Issue 515`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
840 * Improved log messages during shed operations. 08c067c_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
841 * Update tool XSD against latest Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
842 fca4183_, 03c9658_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
843 * Fix bug where ``shed_lint --tools`` for a suite lints the same tools multiple
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
844 times.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
845 `Issue 564`_, `Pull Request 628`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
846
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
847 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
848 0.37.0 (2017-01-25)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
849 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
850
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
851 * Update to the latest `galaxy-lib`_ release. This means new installs start with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
852 Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
853 Conda_ related bugs.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
854 * Change defaults so that Conda automatically initializes and performs tool installs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
855 by default from within the spawned Galaxy server. The trio of flags
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
856 ``--conda_dependency_resolution``, ``--conda_auto_install``, and ``--conda_auto_init``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
857 are effectively enabled by default now. 4595953_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
858 * Use the Galaxy cached dependency manager by default (thanks to `@abretaud`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
859 `Pull Request 612`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
860 * Test Conda dependency resolution for more versions of Galaxy including the forthcoming
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
861 release of 17.01.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
862 * Update to the latest Galaxy tool XSD for various tool linting fixes. 32acd68_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
863 * Fix pip ignores for ``bioconda_scripts`` (thanks to `@nturaga`_)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
864 `Pull Request 614`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
865
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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866 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
867 0.36.1 (2016-12-12)
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parents:
diff changeset
868 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
869
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
870 * Fix move error when using ``project_init``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
871 `Issue 388`_, `Pull Request 610`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
872 * Improved integration testing for ``test`` command. `Pull Request 609`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
873 * Update CWL links to v1.0 (thanks to `@mr-c`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
874 `Pull Request 608`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
875
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
876 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
877 0.36.0 (2016-12-11)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
878 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
879
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
880 * Bring in latest tool XSD file from Galaxy (thanks to `@peterjc`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
881 `Pull Request 605`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
882 * PEP8 fixes for various linting problems
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
883 (thanks to `@peterjc`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
884 `Pull Request 606`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
885 * Update tool syntax URL to new URL (thanks to `@mvdbeek`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
886 `Pull Request 602`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
887
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
888 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
889 0.35.0 (2016-11-14)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
890 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
891
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
892 * Native support for building bioconductor tools and recipes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
893 (thanks to `@nturaga`_). `Pull Request 570`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
894 * Fixes for running Galaxy via docker-galaxy-stable (thanks to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
895 `@bgruening`_). 50d3c4a_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
896 * Import order linting fixes (thanks to `@bgruening`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
897
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
898 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
899 0.34.1 (2016-10-12)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
900 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
901
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
902 * Mimic web browser to validate user help URLs fixing `Issue 578`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
903 (thanks to `@peterjc`_). `Pull Request 591`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
904 * Fix for Bioconda recipes depending on ``conda-forge`` (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
905 `Pull Request 590`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
906
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
907
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
908 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
909 0.34.0 (2016-10-05)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
910 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
911
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
912 * Implement ``mull`` command to build containers for tools based on Conda_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
913 recipes matching requirement definitions. 08cef54_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
914 * Implement ``--mulled_containers`` flag on ``test``, ``serve``, and ``run``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
915 commands to run tools in "mulled" containers. Galaxy will first search
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
916 locally cache containers (such as ones built with ``mull``), then search
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
917 the mulled namespace of `quay.io`_, and finally build one on-demand if
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
918 needed using `galaxy-lib`_ and Involucro_ developed by `@thriqon`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
919 * Implement ``--conda_requirements`` flag on ``lint`` command to ensure requirements
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
920 can be resolved in best practice channels. 9da8387_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
921 * Allow ``conda_install`` command over multiple tool paths. 2e4e5fc_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
922 * Update pip_ as part of setting virtual environment in ``Makefile`` target.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
923 19b2ee9_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
924 * Add script to auto-update Bioconda_ recipe for Planemo and open a pull request.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
925 f0da66f_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
926
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
927 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
928 0.33.2 (2016-09-28)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
929 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
930
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
931 * Fix HISTORY.rst link problem that prevented correct display of content on PyPI_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
932
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
933 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
934 0.33.1 (2016-09-28)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
935 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
936
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
937 * Fix ``lint --urls`` false positives by being more restrictive with what is considered a URL
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
938 (fixed by `@hexylena`_ after detailed report from `@peterjc`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
939 `Issue 573`_, `Pull Request 579`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
940
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
941 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
942 0.33.0 (2016-09-23)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
943 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
944
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
945 * Enable XSD validation of tools by default (restore old behavior with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
946 ``planemo lint --no_xsd``). 1ef05d2_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
947 * Implement a ``conda_lint`` command to lint Conda_ recipes based
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
948 on `anaconda-verify`_. 6a6f164_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
949 * Implement ``clone`` and ``pull_request`` commands to ease PRs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
950 (with documentation fixes from `@martenson`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
951 e925ba1_, ea5324f_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
952 * Update `galaxy.xsd`_ to allow version_command's to have an interpreter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
953 attribute. 7cca2e4_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
954 * Apply improvement from `@nsoranzo`_ for Planemo's use of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
955 `git diff <https://git-scm.com/docs/git-diff>`__.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
956 6f91719_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
957 * Pull in downstream refactoring of ``tool_init`` code from `@nturaga`_'s
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
958 Bioconductor_ work. ccdd2d5_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
959 * Update to latest `Tool Factory`_ code from `tools-iuc`_. ca88b0c_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
960 * Small code cleanups. b6d8294_, d6da3a8_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
961 * Fixup docs in ``planemo.xml.validation``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
962 * Allow skipping newly required lxml_ dependency in `setup.py`_. 34538de_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
963
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
964 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
965 0.32.0 (2016-09-16)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
966 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
967
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
968 * Enhance ``planemo lint --xsd`` to use a fairly complete and newly official XSD
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
969 definition. `Pull Request 566`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
970 * Migrate and update documentation related to tool XML macros and handling
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
971 multiple outputs from the Galaxy wiki (with help from `@bgruening`_, `@mvdbeek`_,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
972 and `@nsoranzo`_). `Pull Request 559`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
973 * Documentation fixes (thanks to `@ramezrawas`_). `Pull Request 561`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
974 * Do not fail URL linting in case of too many requests (thanks to `@nsoranzo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
975 `Pull Request 565`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
976
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
977 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
978 0.31.0 (2016-09-06)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
979 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
980
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
981 * Implement new commands to ``ci_find_repos`` and ``ci_find_tools`` to ease
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
982 CI scripting.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
983 `Pull Request 555`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
984
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
985 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
986 0.30.2 (2016-09-01)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
987 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
988
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
989 * Fix another problem with Conda_ prefix handling when using
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
990 ``--conda_dependency_resolution``. f7b6c7e_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
991
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992 ---------------------
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993 0.30.1 (2016-09-01)
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994 ---------------------
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995
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996 * Fix a problem with Conda_ prefix handling when using
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997 ``--conda_dependency_resolution``. f7b6c7e_
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998 * Fix for quote problem in ``update_planemo_recipe.bash``. 6c03de8_
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999 * Fix to restore linting of ``tests/`` directory and fix import order throughout
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1000 module. ef4b9f4_
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diff changeset
1001
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1002 ---------------------
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diff changeset
1003 0.30.0 (2016-09-01)
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1004 ---------------------
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1005
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1006 * Update to the latest `galaxy-lib`_ release and change Conda_ semantics to match
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diff changeset
1007 recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+
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parents:
diff changeset
1008 with Galaxy 16.07 or master.
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diff changeset
1009 07d94bd_
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diff changeset
1010 * Implement the ``--conda_auto_init`` flag for ``conda_install``. ca19910_
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diff changeset
1011 * Allow the environment variable ``PLANEMO_CONDA_PREFIX`` to set a default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1012 for ``--conda_prefix``.
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diff changeset
1013 24008ab_
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1014 * Fixup documentation regarding installs and Conda_. ce44e87_
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diff changeset
1015 * Fix and lint Python module import order throughout project.
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diff changeset
1016 `Pull Request 550`_
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diff changeset
1017 * Use ``cp`` rather than symlink to ``$DOWNLOAD_CACHE`` in the
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diff changeset
1018 ``dependency_script`` command (thanks to `@peterjc`_). c2204b3_
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1019 * Fixes for the Homebrew recipe updater. c262b6d_
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1020
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1021 ---------------------
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diff changeset
1022 0.29.1 (2016-08-19)
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1023 ---------------------
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1024
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1025 * Improved handling of Python 2.7 specific dependencies.
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diff changeset
1026
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1027 ---------------------
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diff changeset
1028 0.29.0 (2016-08-19)
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diff changeset
1029 ---------------------
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1030
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diff changeset
1031 * Look for sha256sum checksums during shed_lint (thanks to `@peterjc`_).
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parents:
diff changeset
1032 `Pull Request 539`_
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diff changeset
1033 * An assortment fixes and enhancements to the ``dependency_script`` command
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parents:
diff changeset
1034 (thanks to `@peterjc`_). `Pull Request 541`_, `Pull Request 545`_
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1035 * Fix shed_build to respect exclude: in .shed.yml (thanks to `@nsoranzo`_).
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diff changeset
1036 `Pull Request 540`_
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1037 * Fix linting of tool URLs (thanks to `@nsoranzo`_). `Pull Request 546`_
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1038
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1039 ---------------------
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diff changeset
1040 0.28.0 (2016-08-17)
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1041 ---------------------
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1042
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1043 * Fixes for bioblend_ v0.8.0 (thanks to `@nsoranzo`_). 9fdf490_
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1044 * Enable shed repo type update (thanks to `@nsoranzo`_). 3ceaa40_
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diff changeset
1045 * Create suite repositories with repository_suite_definition type by default
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1046 (thanks to `@nsoranzo`_).
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diff changeset
1047 057f4f0_
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1048 * Include ``shed_lint`` in script run by ``travis_init`` (thanks to `@peterjc`_).
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diff changeset
1049 `Pull Request 528`_
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diff changeset
1050 * Minor polish to the ``travis_init`` command (thanks to `@peterjc`_).
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diff changeset
1051 `Pull Request 512`_
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diff changeset
1052 * Update pip_ and setuptools on TravisCI; fix travis_init (thanks to `@peterjc`_).
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diff changeset
1053 `Pull Request 521`_
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diff changeset
1054 * Shorten command one line descriptions for main help (thanks to `@peterjc`_).
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diff changeset
1055 `Pull Request 510`_
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diff changeset
1056 * Use ``planemo test --no_cache_galaxy`` under TravisCI (thanks to `@peterjc`_).
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diff changeset
1057 `Pull Request 513`_
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diff changeset
1058 * Improve and fix docs ahead of GCC 2016 (thanks to `@martenson`_).
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diff changeset
1059 `Pull Request 498`_, 725b232_
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diff changeset
1060 * Add description of ``expect_num_outputs`` to planemo FAQ. a066afb_
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parents:
diff changeset
1061 * Revise planemo tools docs to be more explicit about collection identifiers.
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diff changeset
1062 a811e65_
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diff changeset
1063 * Add more docs on existing dynamic tool output features. `Pull Request 526`_
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diff changeset
1064 * Fix serve command doc (thanks to `@nsoranzo`_). 8c088c6_
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parents:
diff changeset
1065 * Fix `make lint-readme` (RST link errors) (thanks to `@peterjc`_).
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diff changeset
1066 `Pull Request 525`_
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diff changeset
1067 * Add union bedgraph example to project templates (for GCC demo example).
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diff changeset
1068 d53bcd6_
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diff changeset
1069 * Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as
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diff changeset
1070 shed categories (thanks to `@bgruening`_, `@gregvonkuster`_, and `@nsoranzo`_).
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diff changeset
1071 e890ab5_, 08bb354_, e2398fb_
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1072 * Remove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to
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diff changeset
1073 Paul Stewart `@pstew`_).
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diff changeset
1074 `Pull Request 507`_
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diff changeset
1075
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diff changeset
1076 ---------------------
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diff changeset
1077 0.27.0 (2016-06-22)
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diff changeset
1078 ---------------------
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diff changeset
1079
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diff changeset
1080 * Use ephemeris to handle syncing shed tools for workflow actions.
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diff changeset
1081 1c6cfbb_
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1082 * More planemo testing enhancements for testing artifacts that aren't
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diff changeset
1083 Galaxy tools. `Pull Request 491`_
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1084 * Implement ``docker_galaxy`` engine type. eb039c0_, `Issue 15`_
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1085 * Enhance profiles to be Dockerized Galaxy-aware. `Pull Request 488`_
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diff changeset
1086 * Add linter for DOI type citation - thanks to `@mvdbeek`_.
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diff changeset
1087 `Pull Request 484`_
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diff changeset
1088
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1089 ---------------------
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diff changeset
1090 0.26.0 (2016-05-20)
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1091 ---------------------
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1092
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1093 * Implement ``Engine`` and ``Runnable`` abstractions - Planemo now has
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diff changeset
1094 beta support for testing Galaxy workflows and CWL_ tools with Galaxy and
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diff changeset
1095 any CWL_ artifact with cwltool_.
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diff changeset
1096 `Pull Request 454`_, 7be1bf5_
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1097 * Fix missing command_line in test output json. e38c436_
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1098 * More explicit Galaxy ``job_conf.xml`` handling, fixes bugs caused by
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1099 ``galaxy_root`` having existing and incompatible ``job_conf.xml`` files
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1100 and makes it possible to specify defaults with fixed server name. c4dfd55_
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1101 * Introduce profile commands (``profile_create``, ``profile_delete``, and
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1102 ``profile_list``) and profile improvements (automatic postgres database
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1103 creation support). `Pull Request 480`_, a87899b_
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1104 * Rework Galaxy test reporting to use structured data instead of XUnit
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1105 data. 4d29bf1_
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1106 * Refactor Galaxy configuration toward support for running Galaxy in
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1107 docker-galaxy-stable. `Pull Request 479`_
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1108
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1109 ---------------------
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diff changeset
1110 0.25.1 (2016-05-11)
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1111 ---------------------
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1112
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1113 * Tweak dependencies to try to fix cwltool_ related issues - such
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1114 as `Issue 475`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1115
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1116 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1117 0.25.0 (2016-05-11)
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parents:
diff changeset
1118 ---------------------
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parents:
diff changeset
1119
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1120 * Implement Galaxy "profiles" - the ability to configure
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1121 perisistent, named environments for ``serve`` and ``test``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1122 5d08b67_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1123 * Greatly improved ``serve`` command - make ``test-data``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1124 available as an FTP folder, (on 16.07) automatically log
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1125 in an admin user, and many more options (such as those
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1126 required for "profiles" and a ``--daemon`` mode).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1127 * Two fixes to ensure more consistent, dependable ``test`` output.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1128 `Pull Request 472`_, f3c6917_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1129 * Add code and documentation for linting (``lint``) and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1130 building (``tool_init``) CWL_ tools. a4e6958_, b0b867e_,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1131 4cd571c_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1132 * If needed for Conda_ workaround, shorten ``config_directory``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1133 path (thanks to `@mvdbeek`_). efc5f30_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1134 * Fix ``--no_cache_galaxy`` option (thanks to Gildas Le
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1135 Corguillé). d8f2038_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1136 * Target draft 3 of CWL_ instead of draft 2. 775bf49_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1137 * Fix ``cwltool`` dependency version - upstream changes broke
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1138 compatibility. `65b999d`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1139 * Add documentation section and slides about recent Galaxy
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1140 tool framework changes (with fix from `@remimarenco`_). 069e7ba_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1141 * Add IUC standards to Planemo docs. 2ae2b49_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1142 * Improve collection-related contents in documentation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1143 (thanks in part to `@martenson`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1144 fea51fc_, 13a5ae7_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1145 * Add documentation on ``GALAXY_SLOTS`` and running planemo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1146 on a cluster. 45135ff_, e0acf91_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1147 * Revise command-line handling framework for consistency and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1148 extension - allow extra options to be configured as
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1149 defaults ``~/.planemo.yml`` including ``--job_config_file``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1150 and Conda_ configuration options. e769118_, 26e378e_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1151 * Fix ``tool_init`` commans options typos (thanks to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1152 Nitesh Turaga). 826d371_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1153 * Refactor galaxy-related modules into submodules of a new
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1154 ``planemo.galaxy`` package. 8e96864_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1155 * Fix error message typo (thanks to `@blankenberg`_). b1c8f1d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1156 * Update documentation for recent command additions. 3f4ab44_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1157 * Rename option ``--galaxy_sqlite_database`` option to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1158 ``--galaxy_database_seed`` and fix it so it actually works.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1159 f7554d1_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1160 * Add ``--extra_tools`` option to ``serve`` command. 02a08a0_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1161 * Update project testing to include linting documentation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1162 (``docs/``), Python import order, and docstrings.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1163 a13a120_, 6e1e726_, 95d5cba_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1164
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1165
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1166 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1167 0.24.2 (2016-04-25)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1168 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1169
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1170 * Revert "check ``.shed.yml`` owner against credentials during shed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1171 creation", test was incorrect and preventing uploads.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1172 `Pull Request 425`_, `Issue 246`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1173
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1174 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1175 0.24.1 (2016-04-08)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1176 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1177
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1178 * Fix test summary report. `Pull Request 429`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1179 * Improve error reporting when running ``shed_test``. ce8e1be_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1180 * Improved code comments and tests for shed related functionality.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1181 89674cb_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1182 * Rev `galaxy-lib`_ dependency to 16.4.1 to fix wget usage in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1183 newer versions of wget. d76b489_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1184
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1185 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1186 0.24.0 (2016-03-29)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1187 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1188
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1189 * Drop support for Python 2.6. 93b7bda_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1190 * A variety of fixes for ``shed_update``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1191 `Pull Request 428`_, `Issue 416`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1192 * Fix reporting of metadata updates for invalid shed updates.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1193 `Pull Request 426`_, `Issue 420`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1194 * Check ``.shed.yml`` owner against credentials during shed creation.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1195 `Pull Request 425`_, `Issue 246`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1196 * Fix logic error if there is a problem with ``shed_create``. 358a42c_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1197 * Tool documentation improvements. 0298510_, a58a3b8_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1198
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1199 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1200 0.23.0 (2016-02-15)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1201 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1202
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1203 * Fix duplicated attributes with Conda_ resolver (thanks
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1204 to Björn Grüning). `Pull Request 403`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1205 * Upgrade to latest version of `galaxy-lib`_ for more linting.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1206 * Attempt to better handle conditional dependency on cwltool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1207
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1208 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1209 0.22.2 (2016-01-14)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1210 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1211
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1212 * Fixed bug targetting forthcoming release of Galaxy 16.01.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1213
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1214 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1215 0.22.1 (2016-01-14)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1216 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1217
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1218 * Fixed problem with PyPI_ build artifacts due to submodule's not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1219 being initialized during previous release.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1220
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1221 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1222 0.22.0 (2016-01-13)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1223 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1224
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1225 * Add ``--skip_venv`` to support running Galaxy 16.01 inside of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1226 conda environments. 9f3957d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1227 * Implement conda support. f99f6c1_, ad3b2f0_, 5e0b6d1_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1228 * Update LICENSE for Planemo to match Galaxy. 15d33c7_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1229 * Depend on new `galaxy-lib`_ on PyPI_ instead of previous hacks....
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1230 `Pull Request 394`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1231 * Fix egg caching against master/15.10. 6d0f502_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1232 * Fix bug causing shed publishing of ``.svn`` directories.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1233 `Issue 391`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1234 * Bug fixes for Conda_ support thanks to `@bgruening`_. 63e456c_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1235 * Fix document issues thanks to `@einon`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1236 `Pull Request 390`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1237 * Improve client for shed publishing to support newer shed backend
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1238 being developed by `@hexylena`_. `Pull Request 394`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1239 * Tool Shed ``repo_id`` change, `@hexylena`_. `Pull Request 398`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1240 * Various other small changes to testing, project structure, and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1241 Python 3 support.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1242
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parents:
diff changeset
1243 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1244 0.21.1 (2015-11-29)
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parents:
diff changeset
1245 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1246
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1247 * Fix serious regression to ``test`` command. 94097c7_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1248 * Small fixes to release process. 4e1377c_, 94645ed_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1249
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parents:
diff changeset
1250 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1251 0.21.0 (2015-11-29)
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parents:
diff changeset
1252 ---------------------
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parents:
diff changeset
1253
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1254 * If ``virtualenv`` not on ``PATH``, have Planemo create one for Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1255 5b97f2e_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1256 * Add documentation section on testing tools installed in an existing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1257 Galaxy instance. 1927168_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1258 * When creating a virtualenv for Galaxy, prefer Python 2.7.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1259 e0577e7_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1260 * Documentation fixes and improvements thanks to `@martenson`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1261 0f8cb10_, 01584c5_, b757791_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1262 * Specify a minimum ``six`` version requirement. 1c7ee5b_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1263 * Add script to test a planemo as a wheel. 6514ff5_, `Issue 184`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1264 * Fix empty macro loading. `Issue 362`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1265 * Fix an issue when you run ``shed_diff --shed_target local`` thanks
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1266 to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1267 `Pull Request 375`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1268 * Fix ``shed_diff`` printing to stdout if ``-o`` isn't specified.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1269 f3394e7_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1270 * Small ``shed_diff`` improvements to XML diffing and XUnit reporting.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1271 af7448c_, 83e227a_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1272 * More logging of ``shed_diff`` results if ``--verbose`` flagged.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1273 9427b47_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1274 * Add ``test_report`` command for rebuilding reports from structured JSON.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1275 99ee51a_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1276 * Fix option bug with Click 6.0 thanks to `@bgruening`_. 2a7c792_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1277 * Improved error messages for test commands. fdce74c_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1278 * Various fixes for Python 3. 2f66fc3_, 7572e99_, 8eda729_, 764ce01_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1279 * Use newer travis container infrastructure for testing. 6d81a94_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1280 * Test case fixes. 98fdc8c_, 0e4f70a_
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shellac
parents:
diff changeset
1281
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1282 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1283 0.20.0 (2015-11-11)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1284 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1285
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1286 * More complete I/O capturing for XUnit. 6409449_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1287 * Check for select parameter without options when linting tools.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1288 `Issue 373`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1289 * Add ``--cwl_engine`` argument to ``cwl_run`` command. dd94ddc_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1290 * Fixes for select parameter linting. 8b31850_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1291 * Fix to demultiplexing repositories after tool uploads. `Issue 361`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1292 * Fix to update planemo for Galaxy wheels. 25ef0d5_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1293 * Various fixes for Python 2.6 and Python 3.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1294 c1713d2_, 916f610_, c444855_
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shellac
parents:
diff changeset
1295
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diff changeset
1296 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1297 0.19.0 (2015-11-03)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1298 ---------------------
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parents:
diff changeset
1299
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1300 * Initial implementation of ``cwl_run`` command that runs a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1301 CWL tool and job file through Galaxy. 49c5c1e_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1302 * Add ``--cwl`` flag to ``serve`` to experimentally serve CWL tools
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1303 in Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1304 `Pull Request 339`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1305 * Implement highly experimental ``cwl_script`` command to convert
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1306 a CWL job to a bash script. 508dce7_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1307 * Add name to all XUnit reports (thanks to `@hexylena`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1308 `Pull Request 343`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1309 * Capture stdout and stderr for ``shed_diff`` and ``shed_update``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1310 XUnit reports. `Pull Request 344`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1311 * More tool linting (conditionals) thanks to `@hexylena`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1312 `Pull Request 350`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1313 * UTF-8 fixes when handling XUnit reports. `Pull Request 345`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1314 * Add `Epigenetics` as Tool Shed category. `Pull Request 351`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1315 * Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to `@natefoo`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1316 `Pull Request 356`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1317 * Add ``--cite_url`` to ``tool_init``. fdb1b51_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1318 * ``tool_init`` bug fix. f854138_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1319 * Fix `setup.py`_ for cwltool and bioblend_ changes. 1a157d4_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1320 * Add option to specify template sqlite database locally. c23569f_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1321 * Add example IPython notebooks to docs. c8640b6_
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parents:
diff changeset
1322
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diff changeset
1323 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1324 0.18.1 (2015-10-22)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1325 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1326
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1327 * Fix issue with test reporting not being populated. 19900a6_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1328
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1329 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1330 0.18.0 (2015-10-20)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1331 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1332
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1333 * Improvements to ``docker_shell`` usability (thanks to `@kellrott`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1334 `Pull Request 334`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1335 * Add docker pull attempt when missing Dockerfile (thanks to `@kellrott`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1336 `Pull Request 333`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1337 * Fix bug inferring which files are tool files (thanks to `@hexylena`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1338 `Pull Request 335`_, `Issue 313`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1339 * Initial work toward automating brew recipe update. 4d6f7d9_, `Issue 329`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1340
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diff changeset
1341 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1342 0.17.0 (2015-10-19)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1343 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1344
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1345 * Implement basic XUnit report option for ``shed_update`` (thanks to `@martenson`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1346 `Pull Request 322`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1347 * Fix issues with producing test outputs. 572e754_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1348 * Xunit reporting improvements - refactoring, times, diff output (thanks to `@hexylena`_).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1349 `Pull Request 330`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1350 * Implement project governance policy and update developer code of conduct to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1351 match that of the Galaxy project. `Pull Request 316`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1352 * Update filters for account for new ``.txt`` and ``.md`` test outputs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1353 (thanks to `@hexylena`_). `Pull Request 327`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1354 * Add verbose logging to galaxy test output handling problems. 5d7db92_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1355 * Flake8 fixes (thanks to `@martenson`_). 949a36d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1356 * Remove uses of deprecated ``mktemp`` Python standard library function
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1357 (thanks to `@hexylena`_). `Pull Request 330`_
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shellac
parents:
diff changeset
1358
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parents:
diff changeset
1359 ---------------------
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parents:
diff changeset
1360 0.16.0 (2015-10-07)
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parents:
diff changeset
1361 ---------------------
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parents:
diff changeset
1362
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1363 * Adding new command ``dependency_script`` to convert Tool Shed dependencies
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1364 into shell scripts - thanks to `@peterjc`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1365 `Pull Request 310`_, f798c7e_, `Issue 303`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1366 * Implement profiles in sheds section of the ``~/.planemo.yml``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1367 `Pull Request 314`_
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parents:
diff changeset
1368
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parents:
diff changeset
1369 ---------------------
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parents:
diff changeset
1370 0.15.0 (2015-10-01)
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parents:
diff changeset
1371 ---------------------
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parents:
diff changeset
1372
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1373 * Template framework for reporting including new markdown and plain
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1374 text reporting options for testing - thanks to `@hexylena`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1375 `Pull Request 304`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1376 * XUnit style reporting for ``shed_diff`` command - thanks to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1377 `@hexylena`_. `Pull Request 305`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1378 * Add new ``shed_build`` command for building repository tarballs -
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1379 thanks to `@kellrott`_. `Pull Request 297`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1380 * Fix exit code handling for ``lint`` commands - thanks to `@mvdbeek`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1381 `Pull Request 292`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1382 * Improved documentation for ``serve`` command - thanks to `@lparsons`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1383 `Pull Request 312`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1384 * Tiny backward compatible Python 3 tweaks for `Tool Factory`_ - thanks
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1385 to `@peterjc`_. dad2d9d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1386 * Fixed detection of virtual environment in ``Makefile`` - thanks to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1387 `@lparsons`_. `Pull Request 311`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1388 * Updates to Galaxy XSD - thanks to `@mr-c`_. `Pull Request 309`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1389 * Allow reading shed key option from an environment variable.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1390 `Pull Request 307`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1391 * Allow specifying host to serve Galaxy using ``-host`` - thanks in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1392 part to `@chambm`_. `Pull Request 301`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1393 * Allow specifying defaults for ``-host`` and ``--port`` in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1394 ``~/.planemo.yml``. `Pull Request 301`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1395 * Improve ``~/.planemo.yml`` sample comments - thanks to `@martenson`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1396 `Pull Request 287`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1397 * Update tool shed categories - thanks to `@bgruening`_. `Pull Request 285`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1398 * Improved output readibility for ``diff`` command - thanks to `@martenson`_. `Pull Request 284`_
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shellac
parents:
diff changeset
1399
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1400 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1401 0.14.0 (2015-08-06)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1402 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1403
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1404 * Allow ``-t`` as shorthand for ``--shed_target`` (thanks to Peter Cock).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1405 `Pull Request 278`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1406 * Fix ``tool_init`` command to use ``from_work_dir`` only if file in command
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1407 (thanks to bug report and initial fix outline by Gildas Le Corguillé).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1408 `Pull Request 277`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1409 * Various documentation fixes (thanks in part to Peter Cock and Daniel
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1410 Blankenberg). `Pull Request 256`_, `Pull Request 253`_, `Pull Request 254`_,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1411 `Pull Request 255`_, `Pull Request 251`_, `Issue 272`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1412
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parents:
diff changeset
1413 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1414 0.13.2 (2015-07-06)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1415 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1416
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1417 * Fix project_init for missing files. cb5b906_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1418 * Various documentation improvements.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1419
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1420 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1421 0.13.1 (2015-07-01)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1422 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1423
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1424 * Fix for ``shed_init`` producing non-standard type hints. `Issue 243`_,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1425 f0610d7_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1426 * Fix tool linting for parameters that define an ``argument`` but not a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1427 ``name``. `Issue 245`_, aad1eed_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1428 * Many doc updates including a tutorial for developing tools in a test-driven
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1429 fashion and instructions for using the planemo appliance through Kitematic
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1430 (with Kitematic screenshots from E. Rasche).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1431
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1432 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1433 0.13.0 (2015-06-28)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1434 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1435
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1436 * If planemo cannot find a Galaxy root, it will now automatically fetch
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1437 one (specifing ``--galaxy_install`` will still force a fetch).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1438 `Pull Request 235`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1439 * `Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>`__
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1440 has been updated to reflect new and vastly improved Docker and Vagrant
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1441 virtual appliances are now available, as well as a new VirtualBox OVA
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1442 variant.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1443 * Update linting for new tool XML features (including ``detect_errors``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1444 and output collections). `Issue 233`_, 334f2d4_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1445 * Fix ``shed_test`` help text. `Issue 223`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1446 * Fix code typo (thanks to Nicola Soranzo). `Pull Request 230`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1447 * Improvements to algorithm used to guess if an XML file is a tool XML file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1448 `Issue 231`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1449 * Fix configuration file handling bug. `Issue 240`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1450
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1451 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1452 0.12.2 (2015-05-23)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1453 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1454
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1455 * Fix ``shed_test`` and ``shed_serve`` for test and local tool sheds.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1456 f3cafaa_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1457
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1458 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1459 0.12.1 (2015-05-21)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1460 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1461
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1462 * Fix to ensure the tab completion script is in the Python source tarball
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1463 (required for setting up tab-completion for Homebrew). 6b4e7a6_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1464
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1465 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1466 0.12.0 (2015-05-21)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1467 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1468
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1469 * Implement a ``--failed`` flag for the ``test`` command to rerun
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1470 previously faied tests. `Pull Request 210`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1471 * Implement ``shed_update`` to upload contents and update repository
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1472 metadata. `Pull Request 216`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1473 * Implement ``shed_test`` and ``shed_serve`` commands to test and view
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1474 published artifacts in the Tool Shed. `Pull Request 213`_, `Issue 176`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1475 * Add shell tab-completion script. 37dcc07_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1476 * Many more commands allow specifing multiple tool and/or repository targets.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1477 `Issue 150`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1478 * Add -m as alias for --message in planemo shed_upload (thanks to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1479 Peter Cock). `Pull Request 200`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1480 * Add ``--ensure_metadata`` option to ``shed_lint`` to ensure ``.shed.yml``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1481 files contain many repository. `Pull Request 215`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1482 * More developer documentation, additional ``make`` targets including ones
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1483 for setting up git pre-commit hooks. cc8abb6_, `Issue 209`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1484 * Small README improvement (thanks to Martin Čech) b53006d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1485 * Fixes for shed operation error handling (thanks to Martin Čech).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1486 `Pull Request 203`_, `Pull Request 206`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1487 * Fix for "smart" ``shed_diff`` not in the repository root directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1488 (thanks to Peter Cock). `Pull Request 207`_, `Issue 205`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1489 * Recursive ``shed_diff`` with directories not yet in Tool Shed.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1490 `Pull Request 208`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1491 * Improve error handling and reporting for problematic ``--shed_target``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1492 values. `Issue 217`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1493 * Fix typos in lint messages. `Issue 211`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1494
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1495
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diff changeset
1496 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1497 0.11.1 (2015-05-12)
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parents:
diff changeset
1498 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1499
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1500 * Fix default behavior for ``planemo lint`` to use current directory if
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1501 explicit paths are not supplied. 1e3668a_
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diff changeset
1502
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1503 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1504 0.11.0 (2015-05-12)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1505 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1506
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1507 * More compact syntax for defining multiple custom inclusions in ``.shed.yml``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1508 files - thanks to Peter Cock. `Issue 180`_, `Pull Request 185`_,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1509 `Pull Request 196`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1510 * Prevent ambigous destinations when defining custom inclusions in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1511 ``.shed.yml``- thanks to Peter Cock. `Pull Request 186`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1512 * ``lint`` now warns if tool ids contain whitespace. `Pull Request 190`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1513 * Handle empty tar-balls gracefully on older Python versions - thanks
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1514 to Peter Cock. `Pull Request 187`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1515 * Tweak quoting in ``cp`` command - thanks to Peter Cock. 6bcf699_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1516 * Fix regression causing testing to no longer produce "pretty" test
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1517 results under certain circumstances. `Issue 188`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1518 * Fix for recursive ``shed_diff`` folder naming. `Issue 192`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1519 * Fix output definitions to ``tool_init`` command. `Issue 189`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1520
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1521 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1522 0.10.0 (2015-05-06)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1523 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1524
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1525 * Extend ``shed_lint`` to check for valid actions in tool_dependencies.xml
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1526 files. 8117e03_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1527 * Extend ``shed_lint`` to check for required files based on repository type.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1528 `Issue 156`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1529 * Ignore common editor backup files during ``shed_upload``. `Issue 179`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1530 * Fix missing file when installing from source via PyPI_. `Issue 181`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1531 * Fix ``lint`` to verify ``data`` inputs specify a ``format`` attribute.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1532 8117e03_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1533 * Docstring fix thanks to `@peterjc`_. fe7ad46_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1534
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1535
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1536 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1537 0.9.0 (2015-05-03)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1538 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1539
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1540 * Add new logo to the README thanks to `@petrkadlec`_ from `puradesign.cz
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1541 <http://puradesign.cz/en>`__ and `@carlfeberhard`_ from the Galaxy Project.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1542 `Issue 108`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1543 * Implement smarter ``shed_diff`` command - it now produces a meaningful
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1544 exit codes and doesn't report differences if these correspond to attributes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1545 that will be automatically populated by the Tool Shed. `Issue 167`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1546 * Use new smarter ``shed_diff`` code to implement a new ``--check_diff``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1547 option for ``shed_upload`` - to check for meaningful differences before
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1548 updating repositories. `Issue 168`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1549 * Record git commit hash during ``shed_upload`` if the ``.shed.yml`` is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1550 located in a git repository. `Issue 170`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1551 * Allow ``shed_`` operations to operate on git URLs directly. `Issue 169`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1552 * Fail if missing file inclusion statements encountered during ``.shed.yml``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1553 repository resolution - bug reported by `@peterjc`_. `Issue 158`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1554 * Improved exception handling for tool shed operations including new
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1555 ``--fail_fast`` command-line option. * `Issue 114`_, `Pull Request 173`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1556 * Implement more validation when using the ``shed_init`` command. 1cd0e2d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1557 * Add ``-r/--recursive`` option to ``shed_download`` and ``shed_diff``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1558 commands and allow these commands to work with ``.shed.yml`` files defining
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1559 multipe repositories. 40a1f57_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1560 * Add ``--port`` option to the ``serve`` and ``tool_factory`` commands.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1561 15804be_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1562 * Fix problem introduced with `setup.py`_ during the 0.9.0 development cycle
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1563 - thanks to `@peterjc`_. `Pull Request 171`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1564 * Fix clone bug introduced during 0.9.0 development cycle - thanks to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1565 `@bgruening`_. `Pull Request 175`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1566
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1567 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1568 0.8.4 (2015-04-30)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1569 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1570
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1571 * Fix for Travis CI testing picking up invalid tests (reported by `@takadonet`_). `Issue 161`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1572 * Fix tar ordering for consistency (always sort by name) - thanks to `@peterjc`_. `Pull Request 164`_, `Issue 159`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1573 * Fix exception handling related to tool shed operations - thanks to `@peterjc`_. `Pull Request 155`_, b86fe1f_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1574
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1575 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1576 0.8.3 (2015-04-29)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1577 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1578
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1579 * Fix bug where ``shed_lint`` was not respecting the ``-r/--recursive`` flag.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1580 9ff0d2d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1581 * Fix bug where planemo was producing tar files incompatible with the Tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1582 Shed for package and suite repositories. a2ee135_
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1583
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1584 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1585 0.8.2 (2015-04-29)
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diff changeset
1586 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1587
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1588 * Fix bug with ``config_init`` command thanks to `@bgruening`_. `Pull Request 151`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1589 * Fix unnessecary ``lint`` warning about ``parallelism`` tag reported by
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1590 `@peterjc`_. 9bf1eab_
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parents:
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1591
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1592 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1593 0.8.1 (2015-04-28)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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1594 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1595
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1596 * Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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1597
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1598 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1599 0.8.0 (2015-04-27)
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1600 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1601
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1602 * Implement the new ``shed_lint`` command that verifies various aspects of tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1603 shed repositories - including XSD_ validation of ``repository_dependencies.xml``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1604 and ``tool_dependencies.xml`` files, best practices for README files, and the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1605 contents of ``.shed.yml`` files. This requires the lxml_ library to be available
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1606 to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1607 `Issue 89`_ `Issue 91`_ 912df02_ d26929e_ 36ac6d8_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1608 * Option to enable experimental XSD_ based validation of tools when ``lint``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1609 is executed with the new ``--xsd`` flag. This validation occurs against the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1610 unofficial `Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>`__
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1611 maintained by `@JeanFred`_. This requires the lxml_ library to be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1612 available to Planemo or the application xmllint_ to be on its ``PATH``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1613 `Pull Request 130`_ 912df02_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1614 * Allow skipping specific linters when using the ``lint`` command using the new
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1615 ``--skip`` option. 26e3cdb_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1616 * Implement sophisticated options in ``.shed.yml`` to map a directory to many,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1617 custom Tool Shed repositories during shed operaitons such ``shed_upload``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1618 including automatically mapping tools to their own directories and automatically
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1619 building suites repositories. `Pull Request 143`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1620 * Make ``shed_upload`` more intelligent when building tar files so that package
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1621 and suite repositories may have README files in source control and they will
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1622 just be filtered out during upload. 53edd99_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1623 * Implement a new ``shed_init`` command that will help bootstrap ``.shed.yml``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1624 files in the specified directory. cc1a447_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1625 * Extend ``shed_init`` to automatically build a ``repository_rependencies.xml``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1626 file corresponding to a Galaxy workflow (``.ga`` file). `Issue 118`_ 988de1d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1627 * In addition to a single file or directory, allow ``lint`` to be passed multiple
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1628 files. 343902d_ `Issue 139`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1629 * Add ``-r/--recursive`` option to ``shed_create`` and ``lint`` commands. 63cd431_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1630 01f2af9_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1631 * Improved output formatting and option to write diffs to a file for the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1632 ``shed_diff`` command. 965511d_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1633 * Fix lint problem when using new Galaxy testing features such as expecting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1634 job failures and verifing job output. `Issue 138`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1635 * Fix typo in ``test`` help thanks to first time contributor `@pvanheus`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1636 `Pull Request 129`_ 1982076_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1637 * Fix NPE on empty ``help`` element when linting tools. `Issue 124`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1638 * Fix ``lint`` warnings when ``configfiles`` are defined in a tool. 1a85493_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1639 * Fix for empty ``.shed.yml`` files. b7d9e96_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1640 * Fix the ``test`` command for newer versions of nose_. 33294d2_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1641 * Update help content and documentation to be clear ``normalize`` should not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1642 be used to update the contents of tool files at this time. 08de8de_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1643 * Warn on unknown ``command`` attributes when linting tools (anything but
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1644 ``interpreter``). 4f61025_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1645 * Various design, documentation (including new documentation on Tool Shed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1646 `publishing <http://planemo.readthedocs.org/en/latest/publishing.html>`__),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1647 and testing related improvements (test coverage has risen from 65% to over
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1648 80% during this release cycle).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1649
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diff changeset
1650 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1651 0.7.0 (2015-04-13)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1652 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1653
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1654 * Implement `shed_create` command to create Tool Shed repositories from
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1655 ``.shed.yml`` files (thanks to E. Rasche). `Pull Request 101`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1656 * Allow automatic creation of missing repositories during ``shed_upload``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1657 with the new ``--force_repository_creation`` flag (thanks to E. Rasche).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1658 `Pull Request 102`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1659 * Allow specifying files to exclude in ``.shed.yml`` when creating tar files
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1660 for ``shed_upload`` (thanks to Björn Grüning). `Pull Request 99`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1661 * Resolve symbolic links when building Tool Shed tar files with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1662 ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 104`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1663 * Add a `Contributor Code of Conduct
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1664 <https://planemo.readthedocs.org/en/latest/conduct.html>`__.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1665 `Pull Request 113`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1666 * Omit ``tool_test_output.json`` from Tool Shed tar file created with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1667 ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 111`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1668 * Update required version of bioblend_ to ``0.5.3``. Fixed `Issue 88`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1669 * Initial work on implementing tests cases for Tool Shed functionality.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1670 182fe57_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1671 * Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1672 * Download Galaxy from the new, official Github repository. 7c69bf6_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1673 * Update travis_test to install stable planemo from PyPI_. 39fedd2_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1674 * Enable caching on ``--install_galaxy`` by default (disable with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1675 ``--no_cache_galaxy``). d755fe7_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1676
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1677 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1678 0.6.0 (2015-03-16)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1679 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1680
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1681 * Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc...
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1682 * Fix ``tool_init`` to quote file names (thanks to Peter Cock). `Pull Request 98`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1683 * Allow ignoring file patterns in ``.shed.yml`` (thanks to Björn Grüning). `Pull Request 99`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1684 * Add ``--macros`` flag to ``tool_init`` command to generate a macro file as part of tool generation. ec6e30f_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1685 * Add linting of tag order for tool XML files. 4823c5e_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1686 * Add linting of ``stdio`` tags in tool XML files. 8207026_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1687 * More tests, much higher test coverage. 0bd4ff0_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1688
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1689 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1690 0.5.0 (2015-02-22)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1691 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1692
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1693 * Implement ``--version`` option. `Issue 78`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1694 * Implement ``--no_cleanup`` option for ``test`` and ``serve`` commands to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1695 persist temp files. 2e41e0a_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1696 * Fix bug that left temp files undeleted. `Issue 80`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1697 * More improvements to release process. fba3874_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1698
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1699 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1700 0.4.2 (2015-02-21)
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parents:
diff changeset
1701 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1702
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1703 * Fix `setup.py`_ for installing non-Python data from PyPI_ (required newer
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1704 for ``tool_factory`` command and reStructuredText linting). Thanks to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1705 Damion Dooley for the bug report. `Issue 83`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1706
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1707 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1708 0.4.1 (2015-02-16)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1709 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1710
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1711 * Fix README.rst so it renders properly on PyPI_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1712
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1713 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1714 0.4.0 (2015-02-16)
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parents:
diff changeset
1715 ---------------------
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diff changeset
1716
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1717 * Implement ``tool_init`` command for bootstrapping creation of new
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1718 tools (with `tutorial <http://planemo.readthedocs.org/en/latest/writing.html>`_.) 78f8274_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1719 * Implement ``normalize`` command for reorganizing tool XML and macro
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1720 debugging. e8c1d45_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1721 * Implement ``tool_factory`` command to spin up Galaxy pre-configured the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1722 `Tool Factory`_. 9e746b4_
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shellac
parents:
diff changeset
1723 * Added basic linting of ``command`` blocks. b8d90ab_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1724 * Improved linting of ``help`` blocks, including verifying valid
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1725 `reStructuredText`. 411a8da_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1726 * Fix bug related to ``serve`` command not killing Galaxy properly when complete. 53a6766_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1727 * Have ``serve`` command display tools at the top level instead of in shallow sections. badc25f_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1728 * Add additional dependencies to ``setup.py`` more functionality works out
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1729 of the box. 85b9614_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1730 * Fix terrible error message related to bioblend_ being unavailable.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1731 `Issue 70`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1732 * Various smaller documentation and project structure improvements.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1733
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diff changeset
1734 ---------------------
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parents:
diff changeset
1735 0.3.1 (2015-02-15)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1736 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1737
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1738 * Fixes to get PyPI_ workflow working properly.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1739
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parents:
diff changeset
1740 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1741 0.3.0 (2015-02-13)
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parents:
diff changeset
1742 ---------------------
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parents:
diff changeset
1743
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1744 * Add option (``-r``) to the ``shed_upload`` command to recursively upload
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1745 subdirectories (thanks to E. Rasche). `Pull Request 68`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1746 * Fix diff formatting in test reports (thanks to E. Rasche).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1747 `Pull Request 63`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1748 * Grab updated test database to speed up testing (thanks to approach from
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1749 E. Rasche and Dannon Baker). `Issue 61`_, dff4f33_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1750 * Fix test data command-line argument name (was ``test-data`` now it is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1751 ``test_data``). 834bfb2_
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parents:
diff changeset
1752 * Use ``tool_data_table_conf.xml.sample`` file if
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1753 ``tool_data_table_conf.xml.test`` is unavailable. Should allow some
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1754 new tools to be tested without modifying Galaxy's global
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1755 ``tool_data_table_conf.xml`` file. ac4f828_
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shellac
parents:
diff changeset
1756
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diff changeset
1757 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1758 0.2.0 (2015-01-13)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1759 ---------------------
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parents:
diff changeset
1760
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1761 * Improvements to way Planemo loads its own copy of Galaxy modules to prevent
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1762 various conflicts when launching Galaxy from Planemo. `Pull Request 56`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1763 * Allow setting various test output options in ``~/.planemo.yml`` and disabling
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1764 JSON output. 21bb463_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1765 * More experimental Brew and Tool Shed options that should not be considered
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1766 part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1767 * Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1768 report.) a4110a8_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1769 * Documentation fixes for tool linting command (thanks to Nicola Soranzo).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1770 `Pull Request 51`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1771
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diff changeset
1772 ---------------------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1773 0.1.0 (2014-12-16)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1774 ---------------------
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diff changeset
1775
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1776 * Moved repository URL to https://github.com/galaxyproject/planemo.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1777 * Support for publishing to the Tool Shed. `Pull Request 6`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1778 * Support for producing diffs (``shed_diff``) between local repositories and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1779 the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1780 * Use tool's local test data when available - add option for configuring
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1781 ``test-data`` target. `Pull Request 1`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1782 * Support for testing tool features dependent on cached data. 44de95c_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1783 * Support for generating XUnit tool test reports. 82e8b1f_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1784 * Prettier HTML reports for tool tests. 05cc9f4_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1785 * Implement ``share_test`` command for embedding test result links in pull
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1786 requests. `Pull Request 40`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1787 * Fix for properly resolving links during Tool Shed publishing (thanks to Dave
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1788 Bouvier). `Pull Request 29`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1789 * Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1790 * Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1791 Blankenberg). a2c13e4_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1792 * Automate more of Travis CI testing so the scripts added to tool repository
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1793 can be smaller. 20a8680_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1794 * Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1795 `Pull Request 23`_
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1796 * Various documentation fixes (thanks to Martin Čech). 36f7cb1_, b9232e5_
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parents:
diff changeset
1797 * Various smaller fixes for Docker support, tool linting, and documentation.
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parents:
diff changeset
1798
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1799 ---------------------
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diff changeset
1800 0.0.1 (2014-10-04)
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diff changeset
1801 ---------------------
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diff changeset
1802
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diff changeset
1803 * Initial work on the project - commands for testing, linting, serving Galaxy
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1804 tools - and more experimental features involving Docker and Homebrew. 7d07782_
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diff changeset
1805
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diff changeset
1806 .. github_links
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parents:
diff changeset
1807 .. _Pull Request 991: https://github.com/galaxyproject/planemo/pull/991
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1808 .. _Pull Request 988: https://github.com/galaxyproject/planemo/pull/988
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1809 .. _Pull Request 989: https://github.com/galaxyproject/planemo/pull/989
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1810 .. _Pull Request 985: https://github.com/galaxyproject/planemo/pull/985
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1811 .. _Pull Request 984: https://github.com/galaxyproject/planemo/pull/984
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1812 .. _Pull Request 986: https://github.com/galaxyproject/planemo/pull/986
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1813 .. _Pull Request 983: https://github.com/galaxyproject/planemo/pull/983
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1814 .. _Pull Request 982: https://github.com/galaxyproject/planemo/pull/982
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1815 .. _Pull Request 980: https://github.com/galaxyproject/planemo/pull/980
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
1816 .. _Pull Request 978: https://github.com/galaxyproject/planemo/pull/978
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1817 .. _Pull Request 979: https://github.com/galaxyproject/planemo/pull/979
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1818 .. _Pull Request 977: https://github.com/galaxyproject/planemo/pull/977
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1819 .. _Pull Request 975: https://github.com/galaxyproject/planemo/pull/975
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1820 .. _Pull Request 974: https://github.com/galaxyproject/planemo/pull/974
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1821 .. _Pull Request 976: https://github.com/galaxyproject/planemo/pull/976
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1822 .. _Pull Request 972: https://github.com/galaxyproject/planemo/pull/972
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1823 .. _Pull Request 973: https://github.com/galaxyproject/planemo/pull/973
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1824 .. _Pull Request 971: https://github.com/galaxyproject/planemo/pull/971
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1825 .. _Pull Request 970: https://github.com/galaxyproject/planemo/pull/970
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1826 .. _Pull Request 968: https://github.com/galaxyproject/planemo/pull/968
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1827 .. _1ab8530: https://github.com/galaxyproject/planemo/commit/1ab8530
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1828 .. _Pull Request 966: https://github.com/galaxyproject/planemo/pull/966
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1829 .. _Pull Request 964: https://github.com/galaxyproject/planemo/pull/964
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1830 .. _Pull Request 963: https://github.com/galaxyproject/planemo/pull/963
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1831 .. _Pull Request 959: https://github.com/galaxyproject/planemo/pull/959
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1832 .. _Pull Request 958: https://github.com/galaxyproject/planemo/pull/958
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1833 .. _Pull Request 950: https://github.com/galaxyproject/planemo/pull/950
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1834 .. _Pull Request 944: https://github.com/galaxyproject/planemo/pull/944
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diff changeset
1835 .. _Pull Request 926: https://github.com/galaxyproject/planemo/pull/926
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1836 .. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1837 .. _Pull Request 938: https://github.com/galaxyproject/planemo/pull/938
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1838 .. _Pull Request 943: https://github.com/galaxyproject/planemo/pull/943
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1839 .. _Pull Request 940: https://github.com/galaxyproject/planemo/pull/940
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1840 .. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1841 .. _Pull Request 935: https://github.com/galaxyproject/planemo/pull/935
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1842 .. _Pull Request 931: https://github.com/galaxyproject/planemo/pull/931
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1843 .. _Pull Request 930: https://github.com/galaxyproject/planemo/pull/930
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1844 .. _Pull Request 913: https://github.com/galaxyproject/planemo/pull/913
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1845 .. _Pull Request 917: https://github.com/galaxyproject/planemo/pull/917
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1846 .. _Pull Request 921: https://github.com/galaxyproject/planemo/pull/921
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1847 .. _Pull Request 918: https://github.com/galaxyproject/planemo/pull/918
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1848 .. _Pull Request 924: https://github.com/galaxyproject/planemo/pull/924
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1849 .. _Pull Request 925: https://github.com/galaxyproject/planemo/pull/925
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1850 .. _Pull Request 912: https://github.com/galaxyproject/planemo/pull/912
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1851 .. _Pull Request 915: https://github.com/galaxyproject/planemo/pull/915
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1852 .. _Pull Request 914: https://github.com/galaxyproject/planemo/pull/914
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1853 .. _07dc6e0: https://github.com/galaxyproject/planemo/commit/07dc6e0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1854 .. _Pull Request 910: https://github.com/galaxyproject/planemo/pull/910
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1855 .. _Pull Request 909: https://github.com/galaxyproject/planemo/pull/909
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1856 .. _Pull Request 908: https://github.com/galaxyproject/planemo/pull/908
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1857 .. _Pull Request 907: https://github.com/galaxyproject/planemo/pull/907
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1858 .. _Pull Request 906: https://github.com/galaxyproject/planemo/pull/906
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1859 .. _Pull Request 902: https://github.com/galaxyproject/planemo/pull/902
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1860 .. _Pull Request 895: https://github.com/galaxyproject/planemo/pull/895
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1861 .. _Issue 845: https://github.com/galaxyproject/planemo/issues/845
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1862 .. _Issue 898: https://github.com/galaxyproject/planemo/issues/898
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1863 .. _Pull Request 899: https://github.com/galaxyproject/planemo/pull/899
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1864 .. _Pull Request 896: https://github.com/galaxyproject/planemo/pull/896
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1865 .. _Pull Request 894: https://github.com/galaxyproject/planemo/pull/894
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1866 .. _Pull Request 876: https://github.com/galaxyproject/planemo/pull/876
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1867 .. _Pull Request 893: https://github.com/galaxyproject/planemo/pull/893
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1868 .. _Pull Request 892: https://github.com/galaxyproject/planemo/pull/892
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1869 .. _Pull Request 891: https://github.com/galaxyproject/planemo/pull/891
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1870 .. _Pull Request 889: https://github.com/galaxyproject/planemo/pull/889
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1871 .. _Pull Request 888: https://github.com/galaxyproject/planemo/pull/888
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1872 .. _Pull Request 887: https://github.com/galaxyproject/planemo/pull/887
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1873 .. _Pull Request 882: https://github.com/galaxyproject/planemo/pull/882
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1874 .. _Pull Request 877: https://github.com/galaxyproject/planemo/pull/877
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1875 .. _Pull Request 874: https://github.com/galaxyproject/planemo/pull/874
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1876 .. _Pull Request 871: https://github.com/galaxyproject/planemo/pull/871
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1877 .. _Pull Request 870: https://github.com/galaxyproject/planemo/pull/870
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1878 .. _Pull Request 864: https://github.com/galaxyproject/planemo/pull/864
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1879 .. _Pull Request 867: https://github.com/galaxyproject/planemo/pull/867
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1880 .. _Pull Request 868: https://github.com/galaxyproject/planemo/pull/868
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1881 .. _bad810a: https://github.com/galaxyproject/planemo/commit/bad810a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1882 .. _Pull Request 851: https://github.com/galaxyproject/planemo/pull/851
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1883 .. _Pull Request 856: https://github.com/galaxyproject/planemo/pull/856
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1884 .. _Pull Request 860: https://github.com/galaxyproject/planemo/pull/860
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1885 .. _Pull Request 866: https://github.com/galaxyproject/planemo/pull/866
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1886 .. _Pull Request 861: https://github.com/galaxyproject/planemo/pull/861
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1887 .. _324c776: https://github.com/galaxyproject/planemo/commit/324c776
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1888 .. _72d2ca7: https://github.com/galaxyproject/planemo/commit/72d2ca7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1889 .. _b12b117: https://github.com/galaxyproject/planemo/commit/b12b117
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1890 .. _016b923: https://github.com/galaxyproject/planemo/commit/016b923
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1891 .. _2002b49: https://github.com/galaxyproject/planemo/commit/2002b49
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1892 .. _Pull Request 843: https://github.com/galaxyproject/planemo/pull/843
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1893 .. _Pull Request 842: https://github.com/galaxyproject/planemo/pull/842
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1894 .. _Pull Request 841: https://github.com/galaxyproject/planemo/pull/841
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1895 .. _Pull Request 847: https://github.com/galaxyproject/planemo/pull/847
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1896 .. _Pull Request 848: https://github.com/galaxyproject/planemo/pull/848
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1897 .. _Pull Request 849: https://github.com/galaxyproject/planemo/pull/849
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1898 .. _Pull Request 850: https://github.com/galaxyproject/planemo/pull/850
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1899 .. _Pull Request 836: https://github.com/galaxyproject/planemo/pull/836
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1900 .. _Pull Request 833: https://github.com/galaxyproject/planemo/pull/833
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1901 .. _Pull Request 837: https://github.com/galaxyproject/planemo/pull/837
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1902 .. _Pull Request 840: https://github.com/galaxyproject/planemo/pull/840
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1903 .. _Pull Request 838: https://github.com/galaxyproject/planemo/pull/838
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1904 .. _Pull Request 834: https://github.com/galaxyproject/planemo/pull/834
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1905 .. _Pull Request 835: https://github.com/galaxyproject/planemo/pull/835
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1906 .. _347c622: https://github.com/galaxyproject/planemo/commit/347c622
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1907 .. _Pull Request 832: https://github.com/galaxyproject/planemo/pull/832
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1908 .. _Pull Request 831: https://github.com/galaxyproject/planemo/pull/831
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1909 .. _Pull Request 830: https://github.com/galaxyproject/planemo/pull/830
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1910 .. _Pull Request 829: https://github.com/galaxyproject/planemo/pull/829
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1911 .. _Pull Request 828: https://github.com/galaxyproject/planemo/pull/828
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1912 .. _Pull Request 826: https://github.com/galaxyproject/planemo/pull/826
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1913 .. _Pull Request 827: https://github.com/galaxyproject/planemo/pull/827
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1914 .. _Pull Request 825: https://github.com/galaxyproject/planemo/pull/825
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1915 .. _Pull Request 820: https://github.com/galaxyproject/planemo/pull/820
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1916 .. _Pull Request 823: https://github.com/galaxyproject/planemo/pull/823
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1917 .. _Pull Request 822: https://github.com/galaxyproject/planemo/pull/822
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1918 .. _a5c72e3: https://github.com/galaxyproject/planemo/commit/a5c72e3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1919 .. _Pull Request 818: https://github.com/galaxyproject/planemo/pull/818
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1920 .. _Pull Request 816: https://github.com/galaxyproject/planemo/pull/816
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1921 .. _Pull Request 817: https://github.com/galaxyproject/planemo/pull/817
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1922 .. _Pull Request 795: https://github.com/galaxyproject/planemo/pull/795
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1923 .. _Pull Request 799: https://github.com/galaxyproject/planemo/pull/799
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1924 .. _Pull Request 800: https://github.com/galaxyproject/planemo/pull/800
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1925 .. _Pull Request 781: https://github.com/galaxyproject/planemo/pull/781
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1926 .. _Pull Request 801: https://github.com/galaxyproject/planemo/pull/801
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1927 .. _Pull Request 802: https://github.com/galaxyproject/planemo/pull/802
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1928 .. _Pull Request 803: https://github.com/galaxyproject/planemo/pull/803
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1929 .. _Pull Request 805: https://github.com/galaxyproject/planemo/pull/805
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1930 .. _Pull Request 806: https://github.com/galaxyproject/planemo/pull/806
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1931 .. _Pull Request 809: https://github.com/galaxyproject/planemo/pull/809
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1932 .. _Pull Request 810: https://github.com/galaxyproject/planemo/pull/810
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1933 .. _Pull Request 787: https://github.com/galaxyproject/planemo/pull/787
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1934 .. _Pull Request 792: https://github.com/galaxyproject/planemo/pull/792
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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1935 .. _dc443d6: https://github.com/galaxyproject/planemo/commit/dc443d6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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1936 .. _8cfe9e9: https://github.com/galaxyproject/planemo/commit/8cfe9e9
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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1937 .. _41f7df1: https://github.com/galaxyproject/planemo/commit/41f7df1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1938 .. _Pull Request 790: https://github.com/galaxyproject/planemo/pull/790
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1939 .. _Pull Request 776: https://github.com/galaxyproject/planemo/pull/776
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1940 .. _Pull Request 774: https://github.com/galaxyproject/planemo/pull/774
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1941 .. _Pull Request 773: https://github.com/galaxyproject/planemo/pull/773
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1942 .. _Pull Request 771: https://github.com/galaxyproject/planemo/pull/771
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1943 .. _Pull Request 770: https://github.com/galaxyproject/planemo/pull/770
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1944 .. _Pull Request 769: https://github.com/galaxyproject/planemo/pull/769
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1945 .. _Pull Request 768: https://github.com/galaxyproject/planemo/pull/768
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1946 .. _Pull Request 764: https://github.com/galaxyproject/planemo/pull/764
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1947 .. _Pull Request 761: https://github.com/galaxyproject/planemo/pull/761
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1948 .. _Pull Request 759: https://github.com/galaxyproject/planemo/pull/759
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1949 .. _Pull Request 756: https://github.com/galaxyproject/planemo/pull/756
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1950 .. _Pull Request 753: https://github.com/galaxyproject/planemo/pull/753
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1951 .. _Pull Request 747: https://github.com/galaxyproject/planemo/pull/747
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1952 .. _Pull Request 745: https://github.com/galaxyproject/planemo/pull/745
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1953 .. _Pull Request 743: https://github.com/galaxyproject/planemo/pull/743
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1954 .. _Pull Request 739: https://github.com/galaxyproject/planemo/pull/739
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1955 .. _Pull Request 738: https://github.com/galaxyproject/planemo/pull/738
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1956 .. _Pull Request 725: https://github.com/galaxyproject/planemo/pull/725
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1957 .. _Pull Request 727: https://github.com/galaxyproject/planemo/pull/727
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1958 .. _Pull Request 729: https://github.com/galaxyproject/planemo/pull/729
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1959 .. _Pull Request 730: https://github.com/galaxyproject/planemo/pull/730
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1960 .. _Pull Request 731: https://github.com/galaxyproject/planemo/pull/731
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1961 .. _Pull Request 733: https://github.com/galaxyproject/planemo/pull/733
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1962 .. _Pull Request 732: https://github.com/galaxyproject/planemo/pull/732
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1963 .. _Pull Request 704: https://github.com/galaxyproject/planemo/pull/704
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1964 .. _Pull Request 709: https://github.com/galaxyproject/planemo/pull/709
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1965 .. _Pull Request 715: https://github.com/galaxyproject/planemo/pull/715
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1966 .. _Pull Request 716: https://github.com/galaxyproject/planemo/pull/716
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1967 .. _Pull Request 720: https://github.com/galaxyproject/planemo/pull/720
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1968 .. _Pull Request 723: https://github.com/galaxyproject/planemo/pull/723
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1969 .. _8a608e0: https://github.com/galaxyproject/planemo/commit/8a608e0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
1970 .. _ecc1bc2: https://github.com/galaxyproject/planemo/commit/ecc1bc2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1971 .. _Pull Request 702: https://github.com/galaxyproject/planemo/pull/702
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1972 .. _Pull Request 701: https://github.com/galaxyproject/planemo/pull/701
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1973 .. _Pull Request 699: https://github.com/galaxyproject/planemo/pull/699
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1974 .. _91b6fa0: https://github.com/galaxyproject/planemo/commit/91b6fa0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1975 .. _904d77a: https://github.com/galaxyproject/planemo/commit/904d77a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1976 .. _9636682: https://github.com/galaxyproject/planemo/commit/9636682
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1977 .. _475104c: https://github.com/galaxyproject/planemo/commit/475104c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1978 .. _Pull Request 684: https://github.com/galaxyproject/planemo/pull/684
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1979 .. _Pull Request 687: https://github.com/galaxyproject/planemo/pull/687
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1980 .. _Pull Request 688: https://github.com/galaxyproject/planemo/pull/688
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1981 .. _Pull Request 689: https://github.com/galaxyproject/planemo/pull/689
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1982 .. _Pull Request 690: https://github.com/galaxyproject/planemo/pull/690
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1983 .. _Issue 494: https://github.com/galaxyproject/planemo/issues/494
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1984 .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1985 .. _Pull Request 675: https://github.com/galaxyproject/planemo/pull/675
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1986 .. _Pull Request 680: https://github.com/galaxyproject/planemo/pull/680
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1987 .. _Pull Request 682: https://github.com/galaxyproject/planemo/pull/682
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1988 .. _Pull Request 683: https://github.com/galaxyproject/planemo/pull/683
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1989 .. _Pull Request 662: https://github.com/galaxyproject/planemo/pull/662
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1990 .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1991 .. _Pull Request 664: https://github.com/galaxyproject/planemo/pull/664
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1992 .. _84c4a73: https://github.com/galaxyproject/planemo/commit/84c4a73
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1993 .. _32f41c9: https://github.com/galaxyproject/planemo/commit/32f41c9
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1994 .. _3129216: https://github.com/galaxyproject/planemo/commit/3129216
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1995 .. _b4ae44d: https://github.com/galaxyproject/planemo/commit/b4ae44d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1996 .. _3c95b7b: https://github.com/galaxyproject/planemo/commit/3c95b7b
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1997 .. _06bcf19: https://github.com/galaxyproject/planemo/commit/06bcf19
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1998 .. _525de8f: https://github.com/galaxyproject/planemo/commit/525de8f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1999 .. _9867e56: https://github.com/galaxyproject/planemo/commit/9867e56
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2000 .. _ce0dc4e: https://github.com/galaxyproject/planemo/commit/ce0dc4e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2001 .. _4c0f100: https://github.com/galaxyproject/planemo/commit/4c0f100
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2002 .. _04238d3: https://github.com/galaxyproject/planemo/commit/04238d3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2003 .. _ced5ce2: https://github.com/galaxyproject/planemo/commit/ced5ce2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2004 .. _9ab4a0d: https://github.com/galaxyproject/planemo/commit/9ab4a0d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2005 .. _Pull Request 640: https://github.com/galaxyproject/planemo/pull/640
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2006 .. _0a1abfe: https://github.com/galaxyproject/planemo/commit/0a1abfe
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2007 .. _Pull Request 649: https://github.com/galaxyproject/planemo/pull/649
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2008 .. _Issue 620: https://github.com/galaxyproject/planemo/issues/620
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2009 .. _Pull Request 643: https://github.com/galaxyproject/planemo/pull/643
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2010 .. _Pull Request 642: https://github.com/galaxyproject/planemo/pull/642
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2011 .. _Pull Request 641: https://github.com/galaxyproject/planemo/pull/641
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2012 .. _Pull Request 639: https://github.com/galaxyproject/planemo/pull/639
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2013 .. _Pull Request 635: https://github.com/galaxyproject/planemo/pull/635
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2014 .. _Issue 633: https://github.com/galaxyproject/planemo/issues/633
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2015 .. _Issue 260: https://github.com/galaxyproject/planemo/issues/260
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2016 .. _Pull Request 638: https://github.com/galaxyproject/planemo/pull/638
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2017 .. _6638caa: https://github.com/galaxyproject/planemo/commit/6638caa
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2018 .. _8faf661: https://github.com/galaxyproject/planemo/commit/8faf661
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2019 .. _e343b67: https://github.com/galaxyproject/planemo/commit/e343b67
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2020 .. _Pull Request 634: https://github.com/galaxyproject/planemo/pull/634
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2021 .. _84ebc1f: https://github.com/galaxyproject/planemo/commit/84ebc1f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2022 .. _03c9658: https://github.com/galaxyproject/planemo/commit/03c9658
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2023 .. _08c067c: https://github.com/galaxyproject/planemo/commit/08c067c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2024 .. _fca4183: https://github.com/galaxyproject/planemo/commit/fca4183
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2025 .. _Issue 564: https://github.com/galaxyproject/planemo/issues/564
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2026 .. _Pull Request 628: https://github.com/galaxyproject/planemo/pull/628
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2027 .. _Issue 515: https://github.com/galaxyproject/planemo/issues/515
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2028 .. _Pull Request 629: https://github.com/galaxyproject/planemo/pull/629
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2029 .. _Pull Request 614: https://github.com/galaxyproject/planemo/pull/614
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2030 .. _32acd68: https://github.com/galaxyproject/planemo/commit/32acd68
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2031 .. _4595953: https://github.com/galaxyproject/planemo/commit/4595953
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2032 .. _Pull Request 612: https://github.com/galaxyproject/planemo/pull/612
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2033 .. _Issue 388: https://github.com/galaxyproject/planemo/issues/388
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2034 .. _Pull Request 610: https://github.com/galaxyproject/planemo/pull/610
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2035 .. _Pull Request 609: https://github.com/galaxyproject/planemo/pull/609
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2036 .. _Pull Request 608: https://github.com/galaxyproject/planemo/pull/608
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2037 .. _Pull Request 605: https://github.com/galaxyproject/planemo/pull/605
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2038 .. _Pull Request 606: https://github.com/galaxyproject/planemo/pull/606
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2039 .. _Pull Request 602: https://github.com/galaxyproject/planemo/pull/602
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2040 .. _Pull Request 570: https://github.com/galaxyproject/planemo/pull/570
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2041 .. _9228416: https://github.com/galaxyproject/planemo/commit/9228416
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2042 .. _50d3c4a: https://github.com/galaxyproject/planemo/commit/50d3c4a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2043 .. _Issue 578: https://github.com/galaxyproject/planemo/issues/578
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2044 .. _Pull Request 591: https://github.com/galaxyproject/planemo/pull/591
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2045 .. _Pull Request 590: https://github.com/galaxyproject/planemo/pull/590
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2046 .. _f0da66f: https://github.com/galaxyproject/planemo/commit/f0da66f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2047 .. _19b2ee9: https://github.com/galaxyproject/planemo/commit/19b2ee9
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2048 .. _9da8387: https://github.com/galaxyproject/planemo/commit/9da8387
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2049 .. _08cef54: https://github.com/galaxyproject/planemo/commit/08cef54
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2050 .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2051 .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2052 .. _Issue 573: https://github.com/galaxyproject/planemo/issues/573
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2053 .. _Pull Request 579: https://github.com/galaxyproject/planemo/pull/579
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2054 .. _ccdd2d5: https://github.com/galaxyproject/planemo/commit/ccdd2d5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2055 .. _e925ba1: https://github.com/galaxyproject/planemo/commit/e925ba1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2056 .. _ea5324f: https://github.com/galaxyproject/planemo/commit/ea5324f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2057 .. _ca88b0c: https://github.com/galaxyproject/planemo/commit/ca88b0c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2058 .. _b6d8294: https://github.com/galaxyproject/planemo/commit/b6d8294
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2059 .. _6a6f164: https://github.com/galaxyproject/planemo/commit/6a6f164
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2060 .. _d6da3a8: https://github.com/galaxyproject/planemo/commit/d6da3a8
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2061 .. _1ef05d2: https://github.com/galaxyproject/planemo/commit/1ef05d2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2062 .. _7cca2e4: https://github.com/galaxyproject/planemo/commit/7cca2e4
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2063 .. _34538de: https://github.com/galaxyproject/planemo/commit/34538de
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2064 .. _6f91719: https://github.com/galaxyproject/planemo/commit/6f91719
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2065 .. _Pull Request 566: https://github.com/galaxyproject/planemo/pull/566
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2066 .. _Pull Request 559: https://github.com/galaxyproject/planemo/pull/559
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2067 .. _Pull Request 561: https://github.com/galaxyproject/planemo/pull/561
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2068 .. _Pull Request 565: https://github.com/galaxyproject/planemo/pull/565
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2069 .. _Pull Request 555: https://github.com/galaxyproject/planemo/pull/555
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2070 .. _a8e797b: https://github.com/galaxyproject/planemo/commit/a8e797b
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2071 .. _6c03de8: https://github.com/galaxyproject/planemo/commit/6c03de8
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2072 .. _ef4b9f4: https://github.com/galaxyproject/planemo/commit/ef4b9f4
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2073 .. _f7b6c7e: https://github.com/galaxyproject/planemo/commit/f7b6c7e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2074 .. _07d94bd: https://github.com/galaxyproject/planemo/commit/07d94bd
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2075 .. _ca19910: https://github.com/galaxyproject/planemo/commit/ca19910
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2076 .. _24008ab: https://github.com/galaxyproject/planemo/commit/24008ab
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2077 .. _ce44e87: https://github.com/galaxyproject/planemo/commit/ce44e87
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2078 .. _Pull Request 550: https://github.com/galaxyproject/planemo/pull/550
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2079 .. _c2204b3: https://github.com/galaxyproject/planemo/commit/c2204b3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2080 .. _c262b6d: https://github.com/galaxyproject/planemo/commit/c262b6d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2081 .. _Pull Request 539: https://github.com/galaxyproject/planemo/pull/539
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2082 .. _Pull Request 541: https://github.com/galaxyproject/planemo/pull/541
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2083 .. _Pull Request 540: https://github.com/galaxyproject/planemo/pull/540
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2084 .. _Pull Request 545: https://github.com/galaxyproject/planemo/pull/545
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2085 .. _Pull Request 546: https://github.com/galaxyproject/planemo/pull/546
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2086 .. _3ceaa40: https://github.com/galaxyproject/planemo/commit/3ceaa40
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2087 .. _057f4f0: https://github.com/galaxyproject/planemo/commit/057f4f0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2088 .. _9fdf490: https://github.com/galaxyproject/planemo/commit/9fdf490
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2089 .. _8c088c6: https://github.com/galaxyproject/planemo/commit/8c088c6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2090 .. _e2398fb: https://github.com/galaxyproject/planemo/commit/e2398fb
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2091 .. _Pull Request 526: https://github.com/galaxyproject/planemo/pull/526
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2092 .. _Pull Request 528: https://github.com/galaxyproject/planemo/pull/528
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2093 .. _Pull Request 525: https://github.com/galaxyproject/planemo/pull/525
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2094 .. _a811e65: https://github.com/galaxyproject/planemo/commit/a811e65
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2095 .. _Pull Request 521: https://github.com/galaxyproject/planemo/pull/521
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2096 .. _a066afb: https://github.com/galaxyproject/planemo/commit/a066afb
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2097 .. _Pull Request 512: https://github.com/galaxyproject/planemo/pull/512
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2098 .. _08bb354: https://github.com/galaxyproject/planemo/commit/08bb354
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2099 .. _Pull Request 513: https://github.com/galaxyproject/planemo/pull/513
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2100 .. _Pull Request 510: https://github.com/galaxyproject/planemo/pull/510
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2101 .. _e890ab5: https://github.com/galaxyproject/planemo/commit/e890ab5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2102 .. _Pull Request 507: https://github.com/galaxyproject/planemo/pull/507
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2103 .. _d53bcd6: https://github.com/galaxyproject/planemo/commit/d53bcd6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2104 .. _725b232: https://github.com/galaxyproject/planemo/commit/725b232
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2105 .. _Pull Request 498: https://github.com/galaxyproject/planemo/pull/498
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2106 .. _01584c5: https://github.com/galaxyproject/planemo/commit/01584c5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2107 .. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2108 .. _0298510: https://github.com/galaxyproject/planemo/commit/0298510
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2109 .. _02a08a0: https://github.com/galaxyproject/planemo/commit/02a08a0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2110 .. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2111 .. _069e7ba: https://github.com/galaxyproject/planemo/commit/069e7ba
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2112 .. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2113 .. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2114 .. _0e4f70a: https://github.com/galaxyproject/planemo/commit/0e4f70a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2115 .. _0f8cb10: https://github.com/galaxyproject/planemo/commit/0f8cb10
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2116 .. _13a5ae7: https://github.com/galaxyproject/planemo/commit/13a5ae7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2117 .. _15804be: https://github.com/galaxyproject/planemo/commit/15804be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2118 .. _15d33c7: https://github.com/galaxyproject/planemo/commit/15d33c7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2119 .. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2120 .. _1927168: https://github.com/galaxyproject/planemo/commit/1927168
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2121 .. _1982076: https://github.com/galaxyproject/planemo/commit/1982076
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2122 .. _19900a6: https://github.com/galaxyproject/planemo/commit/19900a6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2123 .. _1a157d4: https://github.com/galaxyproject/planemo/commit/1a157d4
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2124 .. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2125 .. _1c6cfbb: https://github.com/galaxyproject/planemo/commit/1c6cfbb
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2126 .. _1c7ee5b: https://github.com/galaxyproject/planemo/commit/1c7ee5b
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2127 .. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2128 .. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2129 .. _2052db0: https://github.com/galaxyproject/planemo/commit/2052db0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2130 .. _20a8680: https://github.com/galaxyproject/planemo/commit/20a86807cb7ea87db2dbc0197ae08a40df3ab2bc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2131 .. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2132 .. _25ef0d5: https://github.com/galaxyproject/planemo/commit/25ef0d5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2133 .. _26e378e: https://github.com/galaxyproject/planemo/commit/26e378e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2134 .. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2135 .. _2a7c792: https://github.com/galaxyproject/planemo/commit/2a7c792
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2136 .. _2ae2b49: https://github.com/galaxyproject/planemo/commit/2ae2b49
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2137 .. _2e41e0a: https://github.com/galaxyproject/planemo/commit/2e41e0a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2138 .. _2f66fc3: https://github.com/galaxyproject/planemo/commit/2f66fc3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2139 .. _30a9c3f: https://github.com/galaxyproject/planemo/commit/30a9c3f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2140 .. _32c6e7f: https://github.com/galaxyproject/planemo/commit/32c6e7f78bb8f04d27615cfd8948b0b89f27b4e6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2141 .. _33294d2: https://github.com/galaxyproject/planemo/commit/33294d2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2142 .. _334f2d4: https://github.com/galaxyproject/planemo/commit/334f2d4
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2143 .. _343902d: https://github.com/galaxyproject/planemo/commit/343902d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2144 .. _3499ca0: https://github.com/galaxyproject/planemo/commit/3499ca0a15affcaf8ac9efc55880da40b0626679
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2145 .. _358a42c: https://github.com/galaxyproject/planemo/commit/358a42c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2146 .. _36ac6d8: https://github.com/galaxyproject/planemo/commit/36ac6d8
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2147 .. _36f7cb1: https://github.com/galaxyproject/planemo/commit/36f7cb114f77731f90860d513a930e10ce5c1ba5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2148 .. _37dcc07: https://github.com/galaxyproject/planemo/commit/37dcc07
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2149 .. _39fedd2: https://github.com/galaxyproject/planemo/commit/39fedd2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2150 .. _3f4ab44: https://github.com/galaxyproject/planemo/commit/3f4ab44
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2151 .. _40a1f57: https://github.com/galaxyproject/planemo/commit/40a1f57
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2152 .. _411a8da: https://github.com/galaxyproject/planemo/commit/411a8da21c92ba37c7ad95bfce9928d9b8fd998e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2153 .. _44de95c: https://github.com/galaxyproject/planemo/commit/44de95c0d7087a5822941959f9a062f6382e329b
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2154 .. _45135ff: https://github.com/galaxyproject/planemo/commit/45135ff
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2155 .. _4823c5e: https://github.com/galaxyproject/planemo/commit/4823c5e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2156 .. _49c5c1e: https://github.com/galaxyproject/planemo/commit/49c5c1e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2157 .. _4c71299: https://github.com/galaxyproject/planemo/commit/4c71299
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2158 .. _4cd571c: https://github.com/galaxyproject/planemo/commit/4cd571c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2159 .. _4d29bf1: https://github.com/galaxyproject/planemo/commit/4d29bf1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2160 .. _4d6f7d9: https://github.com/galaxyproject/planemo/commit/4d6f7d9
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2161 .. _4e1377c: https://github.com/galaxyproject/planemo/commit/4e1377c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2162 .. _4f61025: https://github.com/galaxyproject/planemo/commit/4f61025
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2163 .. _508dce7: https://github.com/galaxyproject/planemo/commit/508dce7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2164 .. _53a6766: https://github.com/galaxyproject/planemo/commit/53a6766cdebdddc976189f6dc6a264bb4105c4bf
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2165 .. _53edd99: https://github.com/galaxyproject/planemo/commit/53edd99
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2166 .. _552059f: https://github.com/galaxyproject/planemo/commit/552059f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2167 .. _572e754: https://github.com/galaxyproject/planemo/commit/572e754
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2168 .. _5b97f2e: https://github.com/galaxyproject/planemo/commit/5b97f2e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2169 .. _5d08b67: https://github.com/galaxyproject/planemo/commit/5d08b67
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2170 .. _5d7db92: https://github.com/galaxyproject/planemo/commit/5d7db92
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2171 .. _5e0b6d1: https://github.com/galaxyproject/planemo/commit/5e0b6d1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2172 .. _63cd431: https://github.com/galaxyproject/planemo/commit/63cd431
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2173 .. _63e456c: https://github.com/galaxyproject/planemo/commit/63e456c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2174 .. _6409449: https://github.com/galaxyproject/planemo/commit/6409449
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2175 .. _6514ff5: https://github.com/galaxyproject/planemo/commit/6514ff5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2176 .. _65b999d: https://github.com/galaxyproject/planemo/commit/65b999d21bacc133a80ecf5f61e0728afec66ccc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2177 .. _6b4e7a6: https://github.com/galaxyproject/planemo/commit/6b4e7a6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2178 .. _6bcf699: https://github.com/galaxyproject/planemo/commit/6bcf699
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2179 .. _6d0f502: https://github.com/galaxyproject/planemo/commit/6d0f502
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2180 .. _6d81a94: https://github.com/galaxyproject/planemo/commit/6d81a94
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2181 .. _6e1e726: https://github.com/galaxyproject/planemo/commit/6e1e726
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2182 .. _7572e99: https://github.com/galaxyproject/planemo/commit/7572e99
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2183 .. _764ce01: https://github.com/galaxyproject/planemo/commit/764ce01
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2184 .. _775bf49: https://github.com/galaxyproject/planemo/commit/775bf49
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2185 .. _776773c: https://github.com/galaxyproject/planemo/commit/776773c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2186 .. _78f8274: https://github.com/galaxyproject/planemo/commit/78f82747996e4a28f96c85ad72efe5e54c8c74bd
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2187 .. _7be1bf5: https://github.com/galaxyproject/planemo/commit/7be1bf5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2188 .. _7c69bf6: https://github.com/galaxyproject/planemo/commit/7c69bf6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2189 .. _7d07782: https://github.com/galaxyproject/planemo/commit/7d077828559c9c9c352ac814f9e3b86b1b3a2a9f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2190 .. _8117e03: https://github.com/galaxyproject/planemo/commit/8117e03
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2191 .. _8207026: https://github.com/galaxyproject/planemo/commit/8207026
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2192 .. _826d371: https://github.com/galaxyproject/planemo/commit/826d371
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2193 .. _82e8b1f: https://github.com/galaxyproject/planemo/commit/82e8b1f17eae526aeb341cb4fffb8d09d73bb419
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2194 .. _834bfb2: https://github.com/galaxyproject/planemo/commit/834bfb2929d367892a3abe9c0b88d5a0277d7905
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2195 .. _83e227a: https://github.com/galaxyproject/planemo/commit/83e227a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2196 .. _85b9614: https://github.com/galaxyproject/planemo/commit/85b961465f46351507f80ddc3758349535060502
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2197 .. _89674cb: https://github.com/galaxyproject/planemo/commit/89674cb
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2198 .. _8b31850: https://github.com/galaxyproject/planemo/commit/8b31850
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2199 .. _8e96864: https://github.com/galaxyproject/planemo/commit/8e96864
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2200 .. _8eda729: https://github.com/galaxyproject/planemo/commit/8eda729
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2201 .. _912df02: https://github.com/galaxyproject/planemo/commit/912df02
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2202 .. _916f610: https://github.com/galaxyproject/planemo/commit/916f610
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2203 .. _93b7bda: https://github.com/galaxyproject/planemo/commit/93b7bda
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2204 .. _94097c7: https://github.com/galaxyproject/planemo/commit/94097c7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2205 .. _9427b47: https://github.com/galaxyproject/planemo/commit/9427b47
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2206 .. _94645ed: https://github.com/galaxyproject/planemo/commit/94645ed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2207 .. _949a36d: https://github.com/galaxyproject/planemo/commit/949a36d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2208 .. _95d5cba: https://github.com/galaxyproject/planemo/commit/95d5cba
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2209 .. _965511d: https://github.com/galaxyproject/planemo/commit/965511d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2210 .. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2211 .. _98fdc8c: https://github.com/galaxyproject/planemo/commit/98fdc8c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2212 .. _99ee51a: https://github.com/galaxyproject/planemo/commit/99ee51a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2213 .. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2214 .. _9e746b4: https://github.com/galaxyproject/planemo/commit/9e746b455e3b15219878cddcdeda722979639401
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2215 .. _9f3957d: https://github.com/galaxyproject/planemo/commit/9f3957d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2216 .. _9ff0d2d: https://github.com/galaxyproject/planemo/commit/9ff0d2d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2217 .. _CWL: http://www.commonwl.org/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2218 .. _Issue 108: https://github.com/galaxyproject/planemo/issues/108
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2219 .. _Issue 114: https://github.com/galaxyproject/planemo/issues/114
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2220 .. _Issue 118: https://github.com/galaxyproject/planemo/issues/118
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2221 .. _Issue 124: https://github.com/galaxyproject/planemo/issues/#124
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2222 .. _Issue 138: https://github.com/galaxyproject/planemo/issues/#138
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2223 .. _Issue 139: https://github.com/galaxyproject/planemo/issues/139
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2224 .. _Issue 150: https://github.com/galaxyproject/planemo/issues/150
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2225 .. _Issue 156: https://github.com/galaxyproject/planemo/issues/156
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2226 .. _Issue 158: https://github.com/galaxyproject/planemo/issues/158
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2227 .. _Issue 159: https://github.com/galaxyproject/planemo/issues/159
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2228 .. _Issue 15: https://github.com/galaxyproject/planemo/issues/15
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2229 .. _Issue 161: https://github.com/galaxyproject/planemo/issues/161
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2230 .. _Issue 167: https://github.com/galaxyproject/planemo/issues/167
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2231 .. _Issue 168: https://github.com/galaxyproject/planemo/issues/168
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2232 .. _Issue 169: https://github.com/galaxyproject/planemo/issues/169
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2233 .. _Issue 170: https://github.com/galaxyproject/planemo/issues/170
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2234 .. _Issue 176: https://github.com/galaxyproject/planemo/issues/176
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2235 .. _Issue 179: https://github.com/galaxyproject/planemo/issues/179
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2236 .. _Issue 180: https://github.com/galaxyproject/planemo/issues/180
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2237 .. _Issue 181: https://github.com/galaxyproject/planemo/issues/181
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2238 .. _Issue 184: https://github.com/galaxyproject/planemo/issues/184
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2239 .. _Issue 186: https://github.com/galaxyproject/planemo/issues/186
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2240 .. _Issue 188: https://github.com/galaxyproject/planemo/issues/188
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2241 .. _Issue 189: https://github.com/galaxyproject/planemo/issues/189
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2242 .. _Issue 192: https://github.com/galaxyproject/planemo/issues/192
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2243 .. _Issue 205: https://github.com/galaxyproject/planemo/issues/205
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2244 .. _Issue 206: https://github.com/galaxyproject/planemo/issues/206
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2245 .. _Issue 209: https://github.com/galaxyproject/planemo/issues/209
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2246 .. _Issue 211: https://github.com/galaxyproject/planemo/issues/211
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2247 .. _Issue 217: https://github.com/galaxyproject/planemo/issues/217
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2248 .. _Issue 223: https://github.com/galaxyproject/planemo/issues/223
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2249 .. _Issue 231: https://github.com/galaxyproject/planemo/issues/231
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2250 .. _Issue 233: https://github.com/galaxyproject/planemo/issues/233
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2251 .. _Issue 240: https://github.com/galaxyproject/planemo/issues/240
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2252 .. _Issue 243: https://github.com/galaxyproject/planemo/issues/243
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2253 .. _Issue 245: https://github.com/galaxyproject/planemo/issues/245
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2254 .. _Issue 246: https://github.com/galaxyproject/planemo/issues/246
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2255 .. _Issue 272: https://github.com/galaxyproject/planemo/issues/272
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2256 .. _Issue 303: https://github.com/galaxyproject/planemo/issues/303
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2257 .. _Issue 313: https://github.com/galaxyproject/planemo/issues/313
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2258 .. _Issue 329: https://github.com/galaxyproject/planemo/issues/329
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2259 .. _Issue 333: https://github.com/galaxyproject/planemo/issues/333
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2260 .. _Issue 361: https://github.com/galaxyproject/planemo/issues/361
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2261 .. _Issue 362: https://github.com/galaxyproject/planemo/issues/362
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2262 .. _Issue 373: https://github.com/galaxyproject/planemo/issues/373
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2263 .. _Issue 391: https://github.com/galaxyproject/planemo/issues/391
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2264 .. _Issue 416: https://github.com/galaxyproject/planemo/issues/416
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2265 .. _Issue 420: https://github.com/galaxyproject/planemo/issues/420
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2266 .. _Issue 475: https://github.com/galaxyproject/planemo/issues/475
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2267 .. _Issue 61: https://github.com/galaxyproject/planemo/issues/61
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2268 .. _Issue 70: https://github.com/galaxyproject/planemo/issues/70
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2269 .. _Issue 78: https://github.com/galaxyproject/planemo/issues/78
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2270 .. _Issue 80: https://github.com/galaxyproject/planemo/issues/80
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2271 .. _Issue 83: https://github.com/galaxyproject/planemo/issues/83
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2272 .. _Issue 88: https://github.com/galaxyproject/planemo/issues/88
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2273 .. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2274 .. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2275 .. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2276 .. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2277 .. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2278 .. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2279 .. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2280 .. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2281 .. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2282 .. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2283 .. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2284 .. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2285 .. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2286 .. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2287 .. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2288 .. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2289 .. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2290 .. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2291 .. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2292 .. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2293 .. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2294 .. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2295 .. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2296 .. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2297 .. _Pull Request 206: https://github.com/galaxyproject/planemo/pull/206
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2298 .. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2299 .. _Pull Request 208: https://github.com/galaxyproject/planemo/pull/208
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2300 .. _Pull Request 210: https://github.com/galaxyproject/planemo/pull/210
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2301 .. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2302 .. _Pull Request 215: https://github.com/galaxyproject/planemo/pull/215
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2303 .. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2304 .. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2305 .. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2306 .. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2307 .. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2308 .. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2309 .. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2310 .. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2311 .. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2312 .. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2313 .. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2314 .. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2315 .. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2316 .. _Pull Request 285: https://github.com/galaxyproject/planemo/pull/285
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2317 .. _Pull Request 287: https://github.com/galaxyproject/planemo/pull/287
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2318 .. _Pull Request 292: https://github.com/galaxyproject/planemo/pull/292
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2319 .. _Pull Request 297: https://github.com/galaxyproject/planemo/pull/297
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2320 .. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2321 .. _Pull Request 301: https://github.com/galaxyproject/planemo/pull/301
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2322 .. _Pull Request 304: https://github.com/galaxyproject/planemo/pull/304
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2323 .. _Pull Request 305: https://github.com/galaxyproject/planemo/pull/305
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2324 .. _Pull Request 307: https://github.com/galaxyproject/planemo/pull/307
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2325 .. _Pull Request 309: https://github.com/galaxyproject/planemo/pull/309
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2326 .. _Pull Request 310: https://github.com/galaxyproject/planemo/pull/310
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2327 .. _Pull Request 311: https://github.com/galaxyproject/planemo/pull/311
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2328 .. _Pull Request 312: https://github.com/galaxyproject/planemo/pull/312
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2329 .. _Pull Request 314: https://github.com/galaxyproject/planemo/pull/314
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2330 .. _Pull Request 316: https://github.com/galaxyproject/planemo/pull/316
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2331 .. _Pull Request 322: https://github.com/galaxyproject/planemo/pull/322
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2332 .. _Pull Request 327: https://github.com/galaxyproject/planemo/pull/327
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2333 .. _Pull Request 330: https://github.com/galaxyproject/planemo/pull/330
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2334 .. _Pull Request 333: https://github.com/galaxyproject/planemo/pull/333
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2335 .. _Pull Request 334: https://github.com/galaxyproject/planemo/pull/334
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2336 .. _Pull Request 335: https://github.com/galaxyproject/planemo/pull/335
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2337 .. _Pull Request 339: https://github.com/galaxyproject/planemo/pull/339
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2338 .. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2339 .. _Pull Request 343: https://github.com/galaxyproject/planemo/pull/343
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2340 .. _Pull Request 344: https://github.com/galaxyproject/planemo/pull/344
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2341 .. _Pull Request 345: https://github.com/galaxyproject/planemo/pull/345
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2342 .. _Pull Request 350: https://github.com/galaxyproject/planemo/pull/350
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2343 .. _Pull Request 351: https://github.com/galaxyproject/planemo/pull/351
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2344 .. _Pull Request 356: https://github.com/galaxyproject/planemo/pull/356
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2345 .. _Pull Request 375: https://github.com/galaxyproject/planemo/pull/375
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2346 .. _Pull Request 390: https://github.com/galaxyproject/planemo/pull/390
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2347 .. _Pull Request 394: https://github.com/galaxyproject/planemo/pull/394
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2348 .. _Pull Request 398: https://github.com/galaxyproject/planemo/pull/398
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2349 .. _Pull Request 403: https://github.com/galaxyproject/planemo/pull/403
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2350 .. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2351 .. _Pull Request 425: https://github.com/galaxyproject/planemo/pull/425
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2352 .. _Pull Request 426: https://github.com/galaxyproject/planemo/pull/426
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2353 .. _Pull Request 428: https://github.com/galaxyproject/planemo/pull/428
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2354 .. _Pull Request 429: https://github.com/galaxyproject/planemo/pull/429
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2355 .. _Pull Request 454: https://github.com/galaxyproject/planemo/pull/454
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2356 .. _Pull Request 472: https://github.com/galaxyproject/planemo/pull/472
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2357 .. _Pull Request 479: https://github.com/galaxyproject/planemo/pull/479
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2358 .. _Pull Request 480: https://github.com/galaxyproject/planemo/pull/480
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2359 .. _Pull Request 484: https://github.com/galaxyproject/planemo/pull/484
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2360 .. _Pull Request 488: https://github.com/galaxyproject/planemo/pull/488
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2361 .. _Pull Request 491: https://github.com/galaxyproject/planemo/pull/491
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2362 .. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2363 .. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2364 .. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2365 .. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2366 .. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2367 .. _Pull Request 98: https://github.com/galaxyproject/planemo/pull/98
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2368 .. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2369 .. _XSD: http://www.w3schools.com/schema/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2370 .. _a13a120: https://github.com/galaxyproject/planemo/commit/a13a120
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2371 .. _a2c13e4: https://github.com/galaxyproject/planemo/commit/a2c13e46259e3be35de1ecaae858ba818bb94734
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2372 .. _a2ee135: https://github.com/galaxyproject/planemo/commit/a2ee135
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2373 .. _a4110a8: https://github.com/galaxyproject/planemo/commit/a4110a85a770988e5cd3c31ccc9475717897d59c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2374 .. _a4e6958: https://github.com/galaxyproject/planemo/commit/a4e6958
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2375 .. _a58a3b8: https://github.com/galaxyproject/planemo/commit/a58a3b8
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2376 .. _a87899b: https://github.com/galaxyproject/planemo/commit/a87899b
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2377 .. _aad1eed: https://github.com/galaxyproject/planemo/commit/aad1eed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2378 .. _ac4f828: https://github.com/galaxyproject/planemo/commit/ac4f82898f7006799142503a33c3978428660ce7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2379 .. _ad3b2f0: https://github.com/galaxyproject/planemo/commit/ad3b2f0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2380 .. _af39061: https://github.com/galaxyproject/planemo/commit/af390612004dab636d8696839bb723d39f97c85d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2381 .. _af7448c: https://github.com/galaxyproject/planemo/commit/af7448c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2382 .. _b0b867e: https://github.com/galaxyproject/planemo/commit/b0b867e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2383 .. _b1c8f1d: https://github.com/galaxyproject/planemo/commit/b1c8f1d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2384 .. _b53006d: https://github.com/galaxyproject/planemo/commit/b53006d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2385 .. _b757791: https://github.com/galaxyproject/planemo/commit/b757791
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2386 .. _b7d9e96: https://github.com/galaxyproject/planemo/commit/b7d9e96
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2387 .. _b86fe1f: https://github.com/galaxyproject/planemo/commit/b86fe1f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2388 .. _b8d90ab: https://github.com/galaxyproject/planemo/commit/b8d90abab8bf53ae2e7cca4317223c01af9ab68c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2389 .. _b9232e5: https://github.com/galaxyproject/planemo/commit/b9232e55e713abbd1d9ce8b0b34cbec6c701dc17
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2390 .. _badc25f: https://github.com/galaxyproject/planemo/commit/badc25fca495b61457ffb2e027f3fe9cf17c798f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2391 .. _bioblend: https://github.com/galaxyproject/bioblend/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2392 .. _c1713d2: https://github.com/galaxyproject/planemo/commit/c1713d2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2393 .. _c23569f: https://github.com/galaxyproject/planemo/commit/c23569f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2394 .. _c444855: https://github.com/galaxyproject/planemo/commit/c444855
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2395 .. _c4dfd55: https://github.com/galaxyproject/planemo/commit/c4dfd55
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2396 .. _c8640b6: https://github.com/galaxyproject/planemo/commit/c8640b6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2397 .. _cb5b906: https://github.com/galaxyproject/planemo/commit/cb5b906
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2398 .. _cc1a447: https://github.com/galaxyproject/planemo/commit/cc1a447
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2399 .. _cc8abb6: https://github.com/galaxyproject/planemo/commit/cc8abb6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2400 .. _ce8e1be: https://github.com/galaxyproject/planemo/commit/ce8e1be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2401 .. _cwltool: https://github.com/common-workflow-language/cwltool/.. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2402 .. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2403 .. _d755fe7: https://github.com/galaxyproject/planemo/commit/d755fe7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2404 .. _d76b489: https://github.com/galaxyproject/planemo/commit/d76b489
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2405 .. _d8f2038: https://github.com/galaxyproject/planemo/commit/d8f2038
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2406 .. _dad2d9d: https://github.com/galaxyproject/planemo/commit/dad2d9d
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2407 .. _dd94ddc: https://github.com/galaxyproject/planemo/commit/dd94ddc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2408 .. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2409 .. _e0577e7: https://github.com/galaxyproject/planemo/commit/e0577e7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2410 .. _e0acf91: https://github.com/galaxyproject/planemo/commit/e0acf91
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2411 .. _e38c436: https://github.com/galaxyproject/planemo/commit/e38c436
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2412 .. _e769118: https://github.com/galaxyproject/planemo/commit/e769118
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2413 .. _e8c1d45: https://github.com/galaxyproject/planemo/commit/e8c1d45f0c9a11bcf69ec2967836c3b8f432dd97
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2414 .. _eb039c0: https://github.com/galaxyproject/planemo/commit/eb039c0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2415 .. _ec6e30f: https://github.com/galaxyproject/planemo/commit/ec6e30f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2416 .. _efc5f30: https://github.com/galaxyproject/planemo/commit/efc5f30
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2417 .. _f0610d7: https://github.com/galaxyproject/planemo/commit/f0610d7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2418 .. _f3394e7: https://github.com/galaxyproject/planemo/commit/f3394e7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2419 .. _f3c6917: https://github.com/galaxyproject/planemo/commit/f3c6917
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2420 .. _f3cafaa: https://github.com/galaxyproject/planemo/commit/f3cafaa
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2421 .. _f7554d1: https://github.com/galaxyproject/planemo/commit/f7554d1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2422 .. _f798c7e: https://github.com/galaxyproject/planemo/commit/f798c7e
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2423 .. _f854138: https://github.com/galaxyproject/planemo/commit/f854138
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2424 .. _f99f6c1: https://github.com/galaxyproject/planemo/commit/f99f6c1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2425 .. _fba3874: https://github.com/galaxyproject/planemo/commit/fba3874
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2426 .. _fdb1b51: https://github.com/galaxyproject/planemo/commit/fdb1b51
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2427 .. _fdce74c: https://github.com/galaxyproject/planemo/commit/fdce74c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2428 .. _fe7ad46: https://github.com/galaxyproject/planemo/commit/fe7ad46
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2429 .. _fea51fc: https://github.com/galaxyproject/planemo/commit/fea51fc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2430 .. _lxml: http://lxml.de/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2431 .. _nose: https://nose.readthedocs.org/en/latest/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2432 .. _xmllint: http://xmlsoft.org/xmllint.html
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2433 .. _Conda: http://conda.pydata.org/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2434 .. _Tool Factory: http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts573.full.pdf
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2435 .. _git: https://git-scm.com/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2436 .. _anaconda-verify: https://github.com/ContinuumIO/anaconda-verify
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2437 .. _galaxy.xsd: https://github.com/galaxyproject/planemo/blob/master/planemo/xml/xsd/tool/galaxy.xsd
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2438 .. _setup.py: https://github.com/galaxyproject/planemo/blob/master/setup.py
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2439 .. _Bioconductor: https://www.bioconductor.org/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2440 .. _tools-iuc: https://github.com/galaxyproject/tools-iuc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2441 .. _PyPI: https://pypi.python.org/pypi
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2442 .. _Involucro: https://github.com/involucro/involucro
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2443 .. _Bioconda: https://bioconda.github.io/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2444 .. _pip: https://pip.pypa.io/en/stable/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2445 .. _BioContainers: http://biocontainers.pro/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2446 .. _Toil: https://github.com/BD2KGenomics/toil
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2447 .. _quay.io: https://quay.io/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2448 .. _galaxy-lib: https://github.com/galaxyproject/galaxy-lib
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2449 .. _@abretaud: https://github.com/abretaud
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2450 .. _@hexylena: https://github.com/hexylena
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2451 .. _@peterjc: https://github.com/peterjc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2452 .. _@mr-c: https://github.com/mr-c
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2453 .. _@martenson: https://github.com/martenson
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2454 .. _@nsoranzo: https://github.com/nsoranzo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2455 .. _@nturaga: https://github.com/nturaga
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2456 .. _@bgruening: https://github.com/bgruening
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2457 .. _@carlfeberhard: https://github.com/carlfeberhard
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2458 .. _@lparsons: https://github.com/lparsons
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2459 .. _@kellrott: https://github.com/kellrott
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2460 .. _@mvdbeek: https://github.com/mvdbeek
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2461 .. _@natefoo: https://github.com/natefoo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2462 .. _@pstew: https://github.com/pstew
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2463 .. _@ramezrawas: https://github.com/ramezrawas
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2464 .. _@chambm: https://github.com/chambm
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2465 .. _@takadonet: https://github.com/takadonet
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2466 .. _@petrkadlec: https://github.com/petrkadlec
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2467 .. _@pvanheus: https://github.com/pvanheus
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2468 .. _@einon: https://github.com/einon
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2469 .. _@blankenberg: https://github.com/blankenberg
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2470 .. _@JeanFred: https://github.com/JeanFred
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2471 .. _@gregvonkuster: https://github.com/gregvonkuster
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2472 .. _@remimarenco: https://github.com/remimarenco
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2473 .. _@thriqon: https://github.com/thriqon
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2474 .. _@RJMW: https://github.com/RJMW
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2475 .. _@manabuishii: https://github.com/manabuishii
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2476 .. _@dfornika: https://github.com/dfornika
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2477 .. _@bernt-matthias: https://github.com/bernt-matthias
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2478 .. _@katrinleinweber: https://github.com/katrinleinweber
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2479 .. _@bebatut: https://github.com/bebatut
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2480 .. _@selten: https://github.com/selten
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2481 .. _@shiltemann: https://github.com/shiltemann
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2482 .. _@bedroesb: https://github.com/bedroesb
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2483 .. _@ic4f: https://github.com/ic4f
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2484 .. _@martin-raden: https://github.com/martin-raden
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2485
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
2486