Mercurial > repos > peterjc > mira_assembler
comparison tools/mira3/README.rst @ 12:63ebe9726219 draft default tip
v0.0.11 move dependency to package_mira_3_4_1_1 etc
author | peterjc |
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date | Wed, 05 Aug 2015 11:28:05 -0400 |
parents | e59904c855ae |
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11:e59904c855ae | 12:63ebe9726219 |
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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 |