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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/samtools_bam2fq commit 7f6d8f6126b7664cccfb987dbec826cf99c7c19a
author | peterjc |
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date | Wed, 13 May 2015 10:22:02 -0400 |
parents | 14ff32f355f0 |
children | 74861ead58ee |
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Galaxy wrapper for samtools bam2fq ==================================== This wrapper 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. This is a wrapper for part of the command line samtools suite. This wrapper is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq WARNING: ``samtools bam2fq`` actually produces a mixture of FASTA and FASTQ depending on if your SAM/BAM input reads have QUAL scores. This is a problem for Galaxy's more rigid datatypes. https://github.com/samtools/samtools/issues/313 Automated Installation ====================== This should be straightforward, Galaxy should automatically download and install samtools 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_bam2fq`` folder: * ``samtools_bam2fq.xml`` (the Galaxy tool definition) * ``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="samtools_bam2fq/samtools_bam2fq.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 samtools_bam2fq That's it. History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial public release, tested with samtools v1.1. v0.0.2 - Defaults to pair-aware mode which requires pre-sorting by read name. v0.0.3 - Faster not to compress intermediate BAM file when sorting. v0.0.4 - Reorder XML elements (internal change only). - lanemo 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/samtools_bam2fq 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_bam2fq/ ... or:: $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_bam2fq/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/samtools_bam2fq/ ... $ tar -tzf shed_upload.tar.gz test-data/sam_spec_padded.bam test-data/sam_spec_padded.bam2fq.fastq test-data/sam_spec_padded.bam2fq_no_suf.fastq test-data/sam_spec_padded.bam2fq_singles.fastq test-data/sam_spec_padded.bam2fq_pairs.fastq test-data/sam_spec_padded.depad.bam test-data/sam_spec_padded.sam tools/samtools_bam2fq/README.rst tools/samtools_bam2fq/samtools_bam2fq.xml tools/samtools_bam2fq/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.