Mercurial > repos > peterjc > coverage_stats
view tools/coverage_stats/README.rst @ 4:c2d0b48203fc draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/coverage_stats commit 3c6f0dca0e1318eecd1e07d177ffc5752b4f6c95
author | peterjc |
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date | Thu, 21 May 2015 10:51:52 -0400 |
parents | 17051c239fdc |
children | 9bc38388d155 |
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BAM coverage statistics using samtools idxstats and depth ========================================================= This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. Internally this tool uses the command-line samtools suite. This tool is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/coverage_stats Automated Installation ====================== This should be straightforward, Galaxy should automatically download and install samtools 0.1.19 if required. Manual Installation =================== This expects samtools to be on the ``$PATH``, and was tested using v0.1.19. To install the wrapper copy or move the following files under the Galaxy tools folder, e.g. in a ``tools/coverage_stats`` folder: * ``coverage_stats.xml`` (the Galaxy tool definition) * ``coverage_stats.py`` (the Python wrapper script) * ``README.rst`` (this file) You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool. Just add the line, perhaps under the NGS tools section:: <tool file="coverage_stats/coverage_stats.xml" /> If you wish to run the unit tests, also move/copy the ``test-data/`` files under Galaxy's ``test-data/`` folder. Then:: $ ./run_tests.sh -id coverage_stats That's it. History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial public release v0.0.2 - Cope with samtools' default depth limit using modified samtools, see https://github.com/samtools/samtools/pull/322 v0.0.3 - Cope with no coverage in final contigs. v0.0.4 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== Developers ========== Development is on this GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats For pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/coverage_stats/ ... or:: $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/coverage_stats/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/coverage_stats/ ... $ tar -tzf shed_upload.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/coverage_test.bam test-data/coverage_test.coverage_stats.tabular test-data/ex1.bam test-data/ex1.coverage_stats.tabular tools/coverage_stats/README.rst tools/coverage_stats/coverage_stats.xml tools/coverage_stats/coverage_stats.py tools/coverage_stats/tool_dependencies.xml Licence (MIT) ============= Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. NOTE: This is the licence for the Galaxy Wrapper only. samtools is available and licenced separately.