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comparison tools/coverage_stats/README.rst @ 2:7254ece0c0ff draft

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v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
author peterjc
date Thu, 11 May 2017 12:16:10 -0400
parents ca8f63f2f7d4
children
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1:d1fdfaae5dbe 2:7254ece0c0ff
1 BAM coverage statistics using samtools idxstats and depth 1 BAM coverage statistics using samtools idxstats and depth
2 ========================================================= 2 =========================================================
3 3
4 This tool is copyright 2014 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2014-2017 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 Internally this tool uses the command-line samtools suite. 8 Internally this tool uses the command-line samtools suite.
9 9
12 12
13 13
14 Automated Installation 14 Automated Installation
15 ====================== 15 ======================
16 16
17 This should be straightforward, Galaxy should automatically download and install 17 This should be straightforward, provided your Galaxy is setup to use Conda and
18 samtools 0.1.19 if required. 18 BioConda for dependencies - Galaxy should then automatically download and
19 install the expected version of samtools.
19 20
20 21
21 Manual Installation 22 Manual Installation
22 =================== 23 ===================
23 24
24 This expects samtools to be on the ``$PATH``, and was tested using v0.1.19. 25 This expects samtools to be on the ``$PATH``, and was tested using v1.3.1.
25 26
26 To install the wrapper copy or move the following files under the Galaxy tools 27 To install the wrapper copy or move the following files under the Galaxy tools
27 folder, e.g. in a ``tools/coverage_stats`` folder: 28 folder, e.g. in a ``tools/coverage_stats`` folder:
28 29
29 * ``coverage_stats.xml`` (the Galaxy tool definition) 30 * ``coverage_stats.xml`` (the Galaxy tool definition)
48 49
49 ======= ====================================================================== 50 ======= ======================================================================
50 Version Changes 51 Version Changes
51 ------- ---------------------------------------------------------------------- 52 ------- ----------------------------------------------------------------------
52 v0.0.1 - Initial public release 53 v0.0.1 - Initial public release
54 v0.0.2 - Cope with samtools' default depth limit using modified samtools,
55 see https://github.com/samtools/samtools/pull/322
56 v0.0.3 - Cope with no coverage in final contigs.
57 v0.0.4 - Reorder XML elements (internal change only).
58 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
59 v0.0.5 - Expose new ``samtools depth -d ...`` argument added in samtools v1.3
60 - Depends on samtools v1.4.1 via Conda, which IS NOT AVAILABLE as a
61 legacy Tool Shed package.
62 - Apply the new maximum depth parameter within the script to ensure
63 excess coverage is clear by getting the max coverage equal to the
64 max depth setting (the raw output from samtools is more fuzzy).
65 - Report total length and overall mean coverage in stdout.
66 - Use ``<command detect_errors="aggressive">`` (internal change only).
67 - Single quote command line arguments (internal change only).
53 ======= ====================================================================== 68 ======= ======================================================================
54 69
55 70
56 Developers 71 Developers
57 ========== 72 ==========
58 73
59 Development is on this GitHub repository: 74 Development is on this GitHub repository:
60 https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 75 https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats
61 76
62 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 77 For pushing a release to the test or main "Galaxy Tool Shed", use the following
63 the following command from the Galaxy root folder:: 78 Planemo commands (which requires you have set your Tool Shed access details in
79 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
64 80
65 $ tar -czf coverage_stats.tar.gz tools/coverage_stats/README.rst tools/coverage_stats/coverage_stats.xml tools/coverage_stats/coverage_stats.py tools/coverage_stats/tool_dependencies.xml test-data/ex1.bam test-data/ex1.coverage_stats.tabular test-data/coverage_test.bam test-data/coverage_test.coverage_stats.tabular 81 $ planemo shed_update -t testtoolshed --check_diff tools/coverage_stats/
82 ...
66 83
67 Check this worked:: 84 or::
68 85
69 $ tar -tzf coverage_stats.tar.gz 86 $ planemo shed_update -t toolshed --check_diff tools/coverage_stats/
87 ...
88
89 To just build and check the tar ball, use::
90
91 $ planemo shed_upload --tar_only tools/coverage_stats/
92 ...
93 $ tar -tzf shed_upload.tar.gz
70 tools/coverage_stats/README.rst 94 tools/coverage_stats/README.rst
71 tools/coverage_stats/coverage_stats.xml 95 tools/coverage_stats/coverage_stats.xml
72 tools/coverage_stats/coverage_stats.py 96 tools/coverage_stats/coverage_stats.py
73 tools/coverage_stats/tool_dependencies.xml 97 ...
74 test-data/ex1.bam
75 test-data/ex1.coverage_stats.tabular
76 test-data/coverage_test.bam
77 test-data/coverage_test.coverage_stats.tabular
78 98
79 99
80 Licence (MIT) 100 Licence (MIT)
81 ============= 101 =============
82 102