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annotate README.rst @ 2:43d6f81bc667 draft

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Updated to Amplicon_Analysis_pipeline v1.2.2.
author pjbriggs
date Wed, 13 Jun 2018 07:45:06 -0400
parents 1c1902e12caf
children 3ab198df8f3f
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1 Amplicon_analysis-galaxy
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2 ========================
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4 A Galaxy tool wrapper to Mauro Tutino's ``Amplicon_analysis`` pipeline
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5 script at https://github.com/MTutino/Amplicon_analysis
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7 The pipeline can analyse paired-end 16S rRNA data from Illumina Miseq
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8 (Casava >= 1.8) and performs the following operations:
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10 * QC and clean up of input data
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11 * Removal of singletons and chimeras and building of OTU table
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12 and phylogenetic tree
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13 * Beta and alpha diversity of analysis
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15 Usage documentation
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16 ===================
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18 Usage of the tool (including required inputs) is documented within
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19 the ``help`` section of the tool XML.
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21 Installing the tool in a Galaxy instance
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22 ========================================
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24 The following sections describe how to install the tool files,
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25 dependencies and reference data, and how to configure the Galaxy
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26 instance to detect the dependencies and reference data correctly
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27 at run time.
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29 1. Install the dependencies
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30 ---------------------------
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32 The ``install_tool_deps.sh`` script can be used to fetch and install the
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33 dependencies locally, for example::
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35 install_tool_deps.sh /path/to/local_tool_dependencies
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37 This can take some time to complete. When finished it should have
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38 created a set of directories containing the dependencies under the
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39 specified top level directory.
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40
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41 2. Install the tool files
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42 -------------------------
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44 The core tool is hosted on the Galaxy toolshed, so it can be installed
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45 directly from there (this is the recommended route):
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47 * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/
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49 Alternatively it can be installed manually; in this case there are two
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50 files to install:
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52 * ``amplicon_analysis_pipeline.xml`` (the Galaxy tool definition)
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53 * ``amplicon_analysis_pipeline.py`` (the Python wrapper script)
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54
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55 Put these in a directory that is visible to Galaxy (e.g. a
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56 ``tools/Amplicon_analysis/`` folder), and modify the ``tools_conf.xml``
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57 file to tell Galaxy to offer the tool by adding the line e.g.::
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58
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59 <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" />
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61 3. Install the reference data
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62 -----------------------------
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64 The script ``References.sh`` from the pipeline package at
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65 https://github.com/MTutino/Amplicon_analysis can be run to install
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66 the reference data, for example::
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67
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68 cd /path/to/pipeline/data
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69 wget https://github.com/MTutino/Amplicon_analysis/raw/master/References.sh
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70 /bin/bash ./References.sh
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72 will install the data in ``/path/to/pipeline/data``.
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73
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74 **NB** The final amount of data downloaded and uncompressed will be
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75 around 6GB.
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77 4. Configure dependencies and reference data in Galaxy
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78 ------------------------------------------------------
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80 The final steps are to make your Galaxy installation aware of the
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81 tool dependencies and reference data, so it can locate them both when
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82 the tool is run.
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84 To target the tool dependencies installed previously, add the
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85 following lines to the ``dependency_resolvers_conf.xml`` file in the
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86 Galaxy ``config`` directory::
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88 <dependency_resolvers>
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89 ...
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90 <galaxy_packages base_path="/path/to/local_tool_dependencies" />
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91 <galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
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92 ...
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93 </dependency_resolvers>
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94
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95 (NB it is recommended to place these *before* the ``<conda ... />``
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96 resolvers)
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97
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98 (If you're not familiar with dependency resolvers in Galaxy then
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99 see the documentation at
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100 https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
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101 for more details.)
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102
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103 The tool locates the reference data via an environment variable called
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104 ``AMPLICON_ANALYSIS_REF_DATA_PATH``, which needs to set to the parent
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105 directory where the reference data has been installed.
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106
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107 There are various ways to do this, depending on how your Galaxy
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108 installation is configured:
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109
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110 * **For local instances:** add a line to set it in the
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111 ``config/local_env.sh`` file of your Galaxy installation, e.g.::
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112
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113 export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data
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114
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115 * **For production instances:** set the value in the ``job_conf.xml``
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116 configuration file, e.g.::
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117
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118 <destination id="amplicon_analysis">
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119 <env id="AMPLICON_ANALYSIS_REF_DATA_PATH">/path/to/pipeline/data</env>
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120 </destination>
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121
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122 and then specify that the pipeline tool uses this destination::
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123
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124 <tool id="amplicon_analysis_pipeline" destination="amplicon_analysis"/>
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125
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126 (For more about job destinations see the Galaxy documentation at
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127 https://galaxyproject.org/admin/config/jobs/#job-destinations)
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128
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129 5. Enable rendering of HTML outputs from pipeline
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130 -------------------------------------------------
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131
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132 To ensure that HTML outputs are displayed correctly in Galaxy
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133 (for example the Vsearch OTU table heatmaps), Galaxy needs to be
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134 configured not to sanitize the outputs from the ``Amplicon_analysis``
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135 tool.
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136
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137 Either:
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138
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139 * **For local instances:** set ``sanitize_all_html = False`` in
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140 ``config/galaxy.ini`` (nb don't do this on production servers or
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141 public instances!); or
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142
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143 * **For production instances:** add the ``Amplicon_analysis`` tool
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144 to the display whitelist in the Galaxy instance:
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145
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146 - Set ``sanitize_whitelist_file = config/whitelist.txt`` in
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147 ``config/galaxy.ini`` and restart Galaxy;
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148 - Go to ``Admin>Manage Display Whitelist``, check the box for
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149 ``Amplicon_analysis`` (hint: use your browser's 'find-in-page'
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150 search function to help locate it) and click on
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151 ``Submit new whitelist`` to update the settings.
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152
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153 Additional details
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154 ==================
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155
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156 Some other things to be aware of:
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157
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158 * Note that using the Silva database requires a minimum of 18Gb RAM
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159
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160 Known problems
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161 ==============
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162
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163 * Only the ``VSEARCH`` pipeline in Mauro's script is currently
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164 available via the Galaxy tool; the ``USEARCH`` and ``QIIME``
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165 pipelines have yet to be implemented.
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166 * The images in the tool help section are not visible if the
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167 tool has been installed locally, or if it has been installed in
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168 a Galaxy instance which is served from a subdirectory.
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169
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170 These are both problems with Galaxy and not the tool, see
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171 https://github.com/galaxyproject/galaxy/issues/4490 and
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172 https://github.com/galaxyproject/galaxy/issues/1676
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173
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174 Appendix: availability of tool dependencies
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175 ===========================================
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176
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177 The tool takes its dependencies from the underlying pipeline script (see
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178 https://github.com/MTutino/Amplicon_analysis/blob/master/README.md
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179 for details).
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180
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181 As noted above, currently the ``install_tool_deps.sh`` script can be
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182 used to manually install the dependencies for a local tool install.
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183
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184 In principle these should also be available if the tool were installed
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185 from a toolshed. However it would be preferrable in this case to get as
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186 many of the dependencies as possible via the ``conda`` dependency
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187 resolver.
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188
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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189 The following are known to be available via conda, with the required
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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190 version:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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191
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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192 - cutadapt 1.8.1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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193 - sickle-trim 1.33
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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194 - bioawk 1.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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195 - fastqc 0.11.3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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196 - R 3.2.0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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197
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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198 Some dependencies are available but with the "wrong" versions:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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199
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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200 - spades (need 3.5.0)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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201 - qiime (need 1.8.0)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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202 - blast (need 2.2.26)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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203 - vsearch (need 1.1.3)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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204
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205 The following dependencies are currently unavailable:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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206
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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207 - fasta_number (need 02jun2015)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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208 - fasta-splitter (need 0.2.4)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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209 - rdp_classifier (need 2.2)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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210 - microbiomeutil (need r20110519)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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211
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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212 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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213 handled outside of Galaxy's dependency management systems.)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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214
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215 History
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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216 =======
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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217
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218 ========== ======================================================================
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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219 Version Changes
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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220 ---------- ----------------------------------------------------------------------
2
43d6f81bc667 Updated to Amplicon_Analysis_pipeline v1.2.2.
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221 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
43d6f81bc667 Updated to Amplicon_Analysis_pipeline v1.2.2.
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222 jackknifed analysis which is not captured by Galaxy tool)
1
1c1902e12caf Updated to version 1.2.1.0
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223 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
1c1902e12caf Updated to version 1.2.1.0
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224 option to use the Human Oral Microbiome Database v15.1, and
1c1902e12caf Updated to version 1.2.1.0
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225 updates SILVA database to v123)
0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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226 1.1.0 First official version on Galaxy toolshed.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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227 1.0.6 Expand inline documentation to provide detailed usage guidance.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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228 1.0.5 Updates including:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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229
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230 - Capture read counts from quality control as new output dataset
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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231 - Capture FastQC per-base quality boxplots for each sample as
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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232 new output dataset
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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233 - Add support for -l option (sliding window length for trimming)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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234 - Default for -L set to "200"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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235 1.0.4 Various updates:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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236
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237 - Additional outputs are captured when a "Categories" file is
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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238 supplied (alpha diversity rarefaction curves and boxplots)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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239 - Sample names derived from Fastqs in a collection of pairs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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240 are trimmed to SAMPLE_S* (for Illumina-style Fastq filenames)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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241 - Input Fastqs can now be of more general ``fastq`` type
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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242 - Log file outputs are captured in new output dataset
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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243 - User can specify a "title" for the job which is copied into
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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244 the dataset names (to distinguish outputs from different runs)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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245 - Improved detection and reporting of problems with input
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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246 Metatable
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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247 1.0.3 Take the sample names from the collection dataset names when
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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248 using collection as input (this is now the default input mode);
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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249 collect additional output dataset; disable ``usearch``-based
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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250 pipelines (i.e. ``UPARSE`` and ``QIIME``).
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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251 1.0.2 Enable support for FASTQs supplied via dataset collections and
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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252 fix some broken output datasets.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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253 1.0.1 Initial version
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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254 ========== ======================================================================