Mercurial > repos > peterjc > coverage_stats
diff tools/coverage_stats/README.rst @ 0:ca8f63f2f7d4 draft
Uploaded v0.0.1
author | peterjc |
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date | Fri, 21 Nov 2014 09:28:29 -0500 |
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children | 7254ece0c0ff |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/coverage_stats/README.rst Fri Nov 21 09:28:29 2014 -0500 @@ -0,0 +1,102 @@ +BAM coverage statistics using samtools idxstats and depth +========================================================= + +This tool is copyright 2014 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 +======= ====================================================================== + + +Developers +========== + +Development is on this GitHub repository: +https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder:: + + $ 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 + +Check this worked:: + + $ tar -tzf 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 + + +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.