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Repository samtools_idxstats
Owner: peterjc
Synopsis: BAM mapping statistics (using samtools idxstats)
Runs "samtools idxstats" to get mapping statistics from a sorted index BAM
file as a tabular output file.
Content homepage:
Type: unrestricted
Revision: 1:8945bad80f4a
This revision can be installed: True
Times cloned / installed: 659

Repository README files - may contain important installation or license information

Galaxy wrapper for samtools idxstats ==================================== This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. This is a wrapper for part of the command line samtools suite, v0.1.19 This wrapper is available from the Galaxy Tool Shed at: 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/samtools_idxstats`` folder: * ``samtools_idxstats.xml`` (the Galaxy tool definition) * ```` (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:: If you wish to run the unit tests, also move/copy the ``test-data/`` files under Galaxy's ``test-data/`` folder. Then:: $ ./ -id samtools_idxstats That's it. History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial public release v0.0.2 - Use quoted filenames when calling samtools (in case of spaces etc) v0.0.3 - Embed samtools citation in tool XML. 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: 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_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/ ... or:: $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/samtools_idxstats/ ... $ tar -tzf shed_upload.tar.gz test-data/ex1.bam test-data/ex1.idxstats.tabular tools/samtools_idxstats/README.rst tools/samtools_idxstats/ tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/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.
Dependencies of this repository

Repository package_samtools_0_1_19 revision c9bd782f5342 owned by iuc

Name Version Type
samtools 0.1.19 package

Contents of this repository

Name Description Version Minimum Galaxy Version
samtools idxstats 0.0.4 any

Assembly - Tools for working with assemblies
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data
SAM - Tools for manipulating alignments in the SAM format