Mercurial > repos > peterjc > coverage_stats
comparison tools/coverage_stats/README.rst @ 4:ed501717f6cd draft default tip
"Update all the pico_galaxy tools on main Tool Shed"
author | peterjc |
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date | Fri, 16 Apr 2021 22:34:30 +0000 |
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1 BAM coverage statistics using samtools idxstats and depth | |
2 ========================================================= | |
3 | |
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. | |
6 See the licence text below. | |
7 | |
8 Internally this tool uses the command-line samtools suite. | |
9 | |
10 This tool is available from the Galaxy Tool Shed at: | |
11 http://toolshed.g2.bx.psu.edu/view/peterjc/coverage_stats | |
12 | |
13 | |
14 Automated Installation | |
15 ====================== | |
16 | |
17 This should be straightforward, provided your Galaxy is setup to use Conda and | |
18 BioConda for dependencies - Galaxy should then automatically download and | |
19 install the expected version of samtools. | |
20 | |
21 | |
22 Manual Installation | |
23 =================== | |
24 | |
25 This expects samtools to be on the ``$PATH``, and was tested using v1.3.1. | |
26 | |
27 To install the wrapper copy or move the following files under the Galaxy tools | |
28 folder, e.g. in a ``tools/coverage_stats`` folder: | |
29 | |
30 * ``coverage_stats.xml`` (the Galaxy tool definition) | |
31 * ``coverage_stats.py`` (the Python wrapper script) | |
32 * ``README.rst`` (this file) | |
33 | |
34 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer | |
35 the tool. Just add the line, perhaps under the NGS tools section:: | |
36 | |
37 <tool file="coverage_stats/coverage_stats.xml" /> | |
38 | |
39 If you wish to run the unit tests, also move/copy the ``test-data/`` files | |
40 under Galaxy's ``test-data/`` folder. Then:: | |
41 | |
42 $ ./run_tests.sh -id coverage_stats | |
43 | |
44 That's it. | |
45 | |
46 | |
47 History | |
48 ======= | |
49 | |
50 ======= ====================================================================== | |
51 Version Changes | |
52 ------- ---------------------------------------------------------------------- | |
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). | |
68 v0.0.6 - Python 3 compatibility fix. | |
69 v0.1.0 - Provide proper command line API for the Python script. | |
70 ======= ====================================================================== | |
71 | |
72 | |
73 Developers | |
74 ========== | |
75 | |
76 Development is on this GitHub repository: | |
77 https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats | |
78 | |
79 For pushing a release to the test or main "Galaxy Tool Shed", use the following | |
80 Planemo commands (which requires you have set your Tool Shed access details in | |
81 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
82 | |
83 $ planemo shed_update -t testtoolshed --check_diff tools/coverage_stats/ | |
84 ... | |
85 | |
86 or:: | |
87 | |
88 $ planemo shed_update -t toolshed --check_diff tools/coverage_stats/ | |
89 ... | |
90 | |
91 To just build and check the tar ball, use:: | |
92 | |
93 $ planemo shed_upload --tar_only tools/coverage_stats/ | |
94 ... | |
95 $ tar -tzf shed_upload.tar.gz | |
96 tools/coverage_stats/README.rst | |
97 tools/coverage_stats/coverage_stats.xml | |
98 tools/coverage_stats/coverage_stats.py | |
99 ... | |
100 | |
101 | |
102 Licence (MIT) | |
103 ============= | |
104 | |
105 Permission is hereby granted, free of charge, to any person obtaining a copy | |
106 of this software and associated documentation files (the "Software"), to deal | |
107 in the Software without restriction, including without limitation the rights | |
108 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
109 copies of the Software, and to permit persons to whom the Software is | |
110 furnished to do so, subject to the following conditions: | |
111 | |
112 The above copyright notice and this permission notice shall be included in | |
113 all copies or substantial portions of the Software. | |
114 | |
115 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
116 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
117 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
118 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
119 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
120 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
121 THE SOFTWARE. | |
122 | |
123 NOTE: This is the licence for the Galaxy Wrapper only. | |
124 samtools is available and licenced separately. |