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comparison tools/samtools_idxstats/README.rst @ 2:71afa65f444a draft default tip

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v0.0.5 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 09:24:18 -0400
parents 8945bad80f4a
children
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1:8945bad80f4a 2:71afa65f444a
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) 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. 54 v0.0.3 - Embed samtools citation in tool XML.
55 v0.0.4 - Reorder XML elements (internal change only). 55 v0.0.4 - Reorder XML elements (internal change only).
56 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). 56 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
57 v0.0.5 - Use ``<command detect_errors="aggressive">`` (internal change only).
58 - Single quote command line arguments (internal change only).
57 ======= ====================================================================== 59 ======= ======================================================================
58 60
59 61
60 Developers 62 Developers
61 ========== 63 ==========
66 68
67 For pushing a release to the test or main "Galaxy Tool Shed", use the following 69 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 70 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):: 71 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
70 72
71 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/ 73 $ planemo shed_update -t testtoolshed --check_diff tools/samtools_idxstats/
72 ... 74 ...
73 75
74 or:: 76 or::
75 77
76 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/ 78 $ planemo shed_update -t toolshed --check_diff tools/samtools_idxstats/
77 ... 79 ...
78 80
79 To just build and check the tar ball, use:: 81 To just build and check the tar ball, use::
80 82
81 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/samtools_idxstats/ 83 $ planemo shed_upload --tar_only tools/samtools_idxstats/
82 ... 84 ...
83 $ tar -tzf shed_upload.tar.gz 85 $ tar -tzf shed_upload.tar.gz
84 test-data/ex1.bam 86 test-data/ex1.bam
85 test-data/ex1.idxstats.tabular 87 test-data/ex1.idxstats.tabular
86 tools/samtools_idxstats/README.rst 88 tools/samtools_idxstats/README.rst