Mercurial > repos > peterjc > effectivet3

comparison tools/effectiveT3/README.rst @ 7:5f85301d50bf draft

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v0.0.16, adding new model TTSS-STD-2.0.2.jar
author peterjc
date Mon, 21 Sep 2015 05:52:29 -0400
parents 0f6eb4a75000
children 60a9b3f760cc
comparison
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6:0f6eb4a75000 7:5f85301d50bf
25 25
26 Automated Installation 26 Automated Installation
27 ====================== 27 ======================
28 28
29 This should be straightforward, Galaxy should automatically download and install 29 This should be straightforward, Galaxy should automatically download and install
30 the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std). 30 the Jar files for effectiveT3 v1.0.1 and its associated models (animal, plant and
31 standard).
31 32
32 33
33 Manual Installation 34 Manual Installation
34 =================== 35 ===================
35 36
71 72
72 ======= ====================================================================== 73 ======= ======================================================================
73 Version Changes 74 Version Changes
74 ------- ---------------------------------------------------------------------- 75 ------- ----------------------------------------------------------------------
75 v0.0.7 - Initial public release 76 v0.0.7 - Initial public release
76 v0.0.8 - Include effectiveT3.loc.sample in Tool Shed 77 v0.0.8 - Include ``effectiveT3.loc.sample`` in Tool Shed
77 v0.0.9 - Check the return code for errors in the XML 78 v0.0.9 - Check the return code for errors in the XML
78 v0.0.10 - Added unit test 79 v0.0.10 - Added unit test
79 v0.0.11 - Automated installation 80 v0.0.11 - Automated installation
80 - Record version of Python script when called from Galaxy 81 - Record version of Python script when called from Galaxy
81 - Link to Tool Shed added to help text and this documentation. 82 - Link to Tool Shed added to help text and this documentation.
87 v0.0.13 - Relax unit test to allow for small floating point score difference. 88 v0.0.13 - Relax unit test to allow for small floating point score difference.
88 - Tool definition now embeds citation information. 89 - Tool definition now embeds citation information.
89 v0.0.14 - Fixed error handling in ``effectiveT3.py``. 90 v0.0.14 - Fixed error handling in ``effectiveT3.py``.
90 v0.0.15 - Reorder XML elements (internal change only). 91 v0.0.15 - Reorder XML elements (internal change only).
91 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). 92 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
93 v0.0.16 - Updated URLs to download the tool and models.
94 - Includes new standard classification model v2.0.2 (Sep 2015)
95 as the default entry in ``tool-data/effectiveT3.loc``
96 - Catch java exception, e.g. if Java too old for ``TTSS-STD-2.0.1.jar``
92 ======= ====================================================================== 97 ======= ======================================================================
93 98
94 99
95 Developers 100 Developers
96 ========== 101 ==========
103 108
104 For pushing a release to the test or main "Galaxy Tool Shed", use the following 109 For pushing a release to the test or main "Galaxy Tool Shed", use the following
105 Planemo commands (which requires you have set your Tool Shed access details in 110 Planemo commands (which requires you have set your Tool Shed access details in
106 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: 111 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
107 112
108 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/ 113 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/
109 ... 114 ...
110 115
111 or:: 116 or::
112 117
113 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/ 118 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/
114 ... 119 ...
115 120
116 To just build and check the tar ball, use:: 121 To just build and check the tar ball, use::
117 122
118 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/effectiveT3/ 123 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/effectiveT3/