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v0.0.4; internal changes for packaging
author peterjc
date Wed, 13 May 2015 10:35:50 -0400
parents d4412c04d7b1
children 71afa65f444a
comparison
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0:d4412c04d7b1 1:8945bad80f4a
1 Galaxy wrapper for samtools idxstats 1 Galaxy wrapper for samtools idxstats
2 ==================================== 2 ====================================
3 3
4 This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute 4 This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below. 6 See the licence text below.
7 7
8 This is a wrapper for part of the command line samtools suite, v0.1.19 8 This is a wrapper for part of the command line samtools suite, v0.1.19
9 9
24 This expects samtools to be on the $PATH, and was tested using v0.1.19. 24 This expects samtools to be on the $PATH, and was tested using v0.1.19.
25 25
26 To install the wrapper copy or move the following files under the Galaxy tools 26 To install the wrapper copy or move the following files under the Galaxy tools
27 folder, e.g. in a ``tools/samtools_idxstats`` folder: 27 folder, e.g. in a ``tools/samtools_idxstats`` folder:
28 28
29 * samtools_idxstats.xml (the Galaxy tool definition) 29 * ``samtools_idxstats.xml`` (the Galaxy tool definition)
30 * samtools_idxstats.py (the Python wrapper script) 30 * ``samtools_idxstats.py`` (the Python wrapper script)
31 * README.rst (this file) 31 * ``README.rst`` (this file)
32 32
33 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer 33 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
34 the tool. Just add the line, perhaps under the NGS tools section:: 34 the tool. Just add the line, perhaps under the NGS tools section::
35 35
36 <tool file="samtools_idxstats/samtools_idxstats.xml" /> 36 <tool file="samtools_idxstats/samtools_idxstats.xml" />
37 37
38 If you wish to run the unit tests, also add this to tools_conf.xml.sample 38 If you wish to run the unit tests, also move/copy the ``test-data/`` files
39 and move/copy the test-data files under Galaxy's test-data folder. Then:: 39 under Galaxy's ``test-data/`` folder. Then::
40 40
41 $ ./run_functional_tests.sh -id samtools_idxstats 41 $ ./run_tests.sh -id samtools_idxstats
42 42
43 That's it. 43 That's it.
44 44
45 45
46 History 46 History
48 48
49 ======= ====================================================================== 49 ======= ======================================================================
50 Version Changes 50 Version Changes
51 ------- ---------------------------------------------------------------------- 51 ------- ----------------------------------------------------------------------
52 v0.0.1 - Initial public release 52 v0.0.1 - Initial public release
53 v0.0.2 - Use quoted filenames when calling samtools (in case of spaces etc)
54 v0.0.3 - Embed samtools citation in tool XML.
55 v0.0.4 - Reorder XML elements (internal change only).
56 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
53 ======= ====================================================================== 57 ======= ======================================================================
54 58
55 59
56 Developers 60 Developers
57 ========== 61 ==========
58 62
59 Development is one this GitHub repository: 63 Development is on this GitHub repository:
60 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 64 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
61 65
62 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
63 the following command from the Galaxy root folder::
64 66
65 $ tar -czf samtools_idxstats.tar.gz tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/tool_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular 67 For pushing a release to the test or main "Galaxy Tool Shed", use the following
68 Planemo commands (which requires you have set your Tool Shed access details in
69 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
66 70
67 Check this worked:: 71 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
72 ...
68 73
69 $ tar -tzf samtools_idxstats.tar.gz 74 or::
70 tools/samtools_idxstats/README.rst 75
71 tools/samtools_idxstats/samtools_idxstats.xml 76 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/
72 tools/samtools_idxstats/samtools_idxstats.py 77 ...
73 tools/samtools_idxstats/tool_dependencies.xml 78
79 To just build and check the tar ball, use::
80
81 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/samtools_idxstats/
82 ...
83 $ tar -tzf shed_upload.tar.gz
74 test-data/ex1.bam 84 test-data/ex1.bam
75 test-data/ex1.idxstats.tabular 85 test-data/ex1.idxstats.tabular
86 tools/samtools_idxstats/README.rst
87 tools/samtools_idxstats/samtools_idxstats.py
88 tools/samtools_idxstats/samtools_idxstats.xml
89 tools/samtools_idxstats/tool_dependencies.xml
76 90
77 91
78 Licence (MIT) 92 Licence (MIT)
79 ============= 93 =============
80 94