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comparison tools/effectiveT3/README.rst @ 5:1ea715da1879 draft

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Uploaded v0.0.13, embed citation, relax test for floating point differences
author peterjc
date Tue, 25 Nov 2014 08:28:24 -0500
parents f7ce32e13bc6
children 0f6eb4a75000
comparison
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4:f7ce32e13bc6 5:1ea715da1879
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33 Manual Installation 33 Manual Installation
34 =================== 34 ===================
35 35
36 You can change the path by setting the environment variable EFFECTIVET3 to the 36 You can change the path by setting the environment variable ``$EFFECTIVET3`` to the
37 relevant folder, but by default it expects the following files to be installed 37 relevant folder, but by default it expects the following files to be installed
38 at these locations:: 38 at these locations::
39 39
40 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar 40 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
41 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar 41 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
43 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar 43 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
44 44
45 To install the wrapper copy or move the following files under the Galaxy tools 45 To install the wrapper copy or move the following files under the Galaxy tools
46 folder, e.g. in a tools/effectiveT3 folder: 46 folder, e.g. in a tools/effectiveT3 folder:
47 47
48 * effectiveT3.xml (the Galaxy tool definition) 48 * ``effectiveT3.xml`` (the Galaxy tool definition)
49 * effectiveT3.py (the Python wrapper script) 49 * ``effectiveT3.py`` (the Python wrapper script)
50 * README.rst (this file) 50 * ``README.rst`` (this file)
51 51
52 Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder 52 Also copy ``effectiveT3.loc.sample`` to ``effectiveT3.loc`` in the ``tool-data``
53 (and edit if appropriate, e.g. to add or remove a model). 53 folder (and edit if appropriate, e.g. to add or remove a model).
54 54
55 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the 55 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
56 tool. If you are using other protein analysis tools like TMHMM or SignalP, put 56 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
57 it next to them. Just add the line:: 57 it next to them. Just add the line::
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59 <tool file="effectiveT3/effectiveT3.xml" /> 59 <tool file="effectiveT3/effectiveT3.xml" />
60 60
61 If you wish to run the unit tests, also add this to tools_conf.xml.sample 61 If you wish to run the unit tests, also move/copy the ``test-data/`` files
62 and move/copy the test-data files under Galaxy's test-data folder. Then:: 62 under Galaxy's ``test-data/`` folder. Then::
63 63
64 $ ./run_functional_tests.sh -id effectiveT3 64 $ ./run_tests.sh -id effectiveT3
65 65
66 That's it. 66 That's it.
67 67
68 68
69 History 69 History
82 v0.0.12 - More explicit naming of the output dataset. 82 v0.0.12 - More explicit naming of the output dataset.
83 - Adopt standard MIT licence. 83 - Adopt standard MIT licence.
84 - Use reStructuredText for this README file. 84 - Use reStructuredText for this README file.
85 - Updated citation information (Cock et al. 2013). 85 - Updated citation information (Cock et al. 2013).
86 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy 86 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
87 v0.0.13 - Relax unit test to allow for small floating point score difference.
88 - Tool definition now embeds citation information.
89 - Fixed error handling in ``effectiveT3.py``.
87 ======= ====================================================================== 90 ======= ======================================================================
88 91
89 92
90 Developers 93 Developers
91 ========== 94 ==========