Mercurial > repos > peterjc > count_roi_variants
view tools/count_roi_variants/README.rst @ 0:95efbdb72961 draft
v0.0.4 - Previously only on Test Tool Shed
author | peterjc |
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date | Wed, 01 Feb 2017 07:10:26 -0500 |
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children | 3ee6f4d0ac80 |
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Count sequence variants in region of interest in BAM file ========================================================= This tool is copyright 2016 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. This tool runs the command ``samtools view`` (taking advantage of an indexed BAM file) to access only those reads mapped to the region of interest (ROI), and then counts the different sequence variants found. 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/count_roi_variants Use outside of Galaxy ===================== You just need the ``count_roi_variants.py`` script and to have samtools on the ``$PATH``. If you move/copy the script somewhere on your ``$PATH`` and then you can run it like this:: $ count_roi_variants.py --help Or, call the script at an explicit path:: $ /path/to/my/stuff/count_roi_variants.py --help Run like this it will use the current default Python. This was written and tested under Python 2.7, but should also work under Python 2.6. e.g.:: $ python2.6 /path/to/my/stuff/count_roi_variants.py --help This does not yet support Python 3. The sample data and tests are designed to be run via Galaxy. Automated Galaxy Installation ============================= This should be straightforward, Galaxy should automatically download and install samtools if required. Manual Galaxy Installation ========================== This expects samtools to be on the ``$PATH``, and was tested using v0.1.3 To install the wrapper copy or move the following files under the Galaxy tools folder, e.g. in a ``tools/count_roi_variants`` folder: * ``count_roi_variants.xml`` (the Galaxy tool definition) * ``count_roi_variants.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="count_roi_variants/count_roi_variants.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 count_roi_variants That's it. History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial public release v0.0.2 - Cope with pipes in reference name (e.g. NCBI style FASTA naming) v0.0.3 - Include a functional test for using an unrecognised reference. v0.0.4 - Improved usage text and README for use outside of Galaxy. ======= ====================================================================== Developers ========== Development is on this GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 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 -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/count_roi_variants/ ... or:: $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/count_roi_variants/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/count_roi_variants/ ... $ tar -tzf shed_upload.tar.gz tools/count_roi_variants/README.rst tools/count_roi_variants/count_roi_variants.xml tools/count_roi_variants/count_roi_variants.py tools/count_roi_variants/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.