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v0.0.11 move dependency to package_mira_3_4_1_1 etc
author peterjc
date Wed, 05 Aug 2015 11:28:05 -0400
parents e59904c855ae
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11:e59904c855ae 12:63ebe9726219
28 28
29 * ``mira.py`` (the Python script) 29 * ``mira.py`` (the Python script)
30 * ``mira.xml`` (the Galaxy tool definition) 30 * ``mira.xml`` (the Galaxy tool definition)
31 31
32 The suggested location is a new ``tools/mira3`` folder. You will also need to 32 The suggested location is a new ``tools/mira3`` folder. You will also need to
33 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do 33 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding
34 this to ``tools_conf.xml.sample`` in order to run any tests:: 34 the line::
35
36 <tool file="mira3/mira.xml" />
35 37
36 <tool file="mira3/mira.xml" /> 38 If you wish to run the unit tests, also move/copy the ``test-data/`` files
39 under Galaxy's ``test-data/`` folder. Then::
40
41 $ ./run_tests -id mira_assembler
37 42
38 You will also need to install MIRA, we used version 3.4.1.1. See: 43 You will also need to install MIRA, we used version 3.4.1.1. See:
39 44
40 * http://chevreux.org/projects_mira.html 45 * http://chevreux.org/projects_mira.html
41 * http://sourceforge.net/projects/mira-assembler/ 46 * http://sourceforge.net/projects/mira-assembler/
75 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy 80 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
76 v0.0.9 - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper). 81 v0.0.9 - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
77 - Correct path issue in automated dependency installation. 82 - Correct path issue in automated dependency installation.
78 v0.0.10 - Added a functional test. 83 v0.0.10 - Added a functional test.
79 - Updated URL for automated installation of MIRA v3.4.1.1 84 - Updated URL for automated installation of MIRA v3.4.1.1
85 v0.0.11 - Tool definition now embeds citation information.
86 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
87 - MIRA 3.4.1.1 dependency now declared via dedicated Tool Shed package.
80 ======= ====================================================================== 88 ======= ======================================================================
81 89
82 90
83 Developers 91 Developers
84 ========== 92 ==========
87 http://bitbucket.org/peterjc/galaxy-central/src/tools 95 http://bitbucket.org/peterjc/galaxy-central/src/tools
88 96
89 Development has now moved to a dedicated GitHub repository: 97 Development has now moved to a dedicated GitHub repository:
90 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4 98 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
91 99
92 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 100 For pushing a release to the test or main "Galaxy Tool Shed", use the following
93 the following command from the Galaxy root folder:: 101 Planemo commands (which requires you have set your Tool Shed access details in
102 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
94 103
95 $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/empty_file.dat 104 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
105 ...
96 106
97 Check this worked:: 107 or::
98 108
99 $ tar -tzf mira3_wrapper.tar.gz 109 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
110 ...
111
112 To just build and check the tar ball, use::
113
114 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mira3/
115 ...
116 $ tar -tzf shed_upload.tar.gz
117 test-data/empty_file.dat
118 test-data/tvc_contigs.fasta
119 test-data/tvc_mini.fastq
100 tools/mira3/README.rst 120 tools/mira3/README.rst
121 tools/mira3/mira.py
101 tools/mira3/mira.xml 122 tools/mira3/mira.xml
102 tools/mira3/mira.py
103 tools/mira3/tool_dependencies.xml 123 tools/mira3/tool_dependencies.xml
104 test-data/tvc_mini.fastq
105 test-data/tvc_contigs.fasta
106 test-data/empty_file.dat
107 124
108 125
109 Licence (MIT) 126 Licence (MIT)
110 ============= 127 =============
111 128