Mercurial > repos > crs4 > bwa_mem
comparison readme.rst @ 0:6820983ba5d5 draft
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| author | crs4 |
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| date | Tue, 18 Mar 2014 07:49:22 -0400 |
| parents | |
| children | ebb02ba5987c |
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| -1:000000000000 | 0:6820983ba5d5 |
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| 1 BWA-MEM wrapper | |
| 2 =============== | |
| 3 | |
| 4 This is a wrapper for BWA_, a software package for mapping low-divergent sequences against a large reference genome. This wrapper supports only the latest algorithm, BWA-MEM, which is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. | |
| 5 | |
| 6 .. _BWA: http://bio-bwa.sourceforge.net/ | |
| 7 | |
| 8 If you need a wrapper for the old BWA-backtrack algorithm, you may install http://toolshed.g2.bx.psu.edu/view/devteam/bwa_wrappers repository. | |
| 9 | |
| 10 Configuration | |
| 11 ------------- | |
| 12 | |
| 13 bwa_mem tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). | |
| 14 | |
| 15 If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool. | |
| 16 | |
| 17 If instead you are using an older Galaxy release, you should also add a line | |
| 18 | |
| 19 GALAXY_SLOTS=N; export GALAXY_SLOTS | |
| 20 | |
| 21 (where N is the number of CPU cores allocated by the job runner for this tool) to the file | |
| 22 | |
| 23 <tool_dependencies_dir>/bwa/0.7.7/crs4/bwa_mem/<hash_string>/env.sh | |
| 24 | |
| 25 Version history | |
| 26 --------------- | |
| 27 | |
| 28 - Release 0: Initial release in the Tool Shed. This is a fork of http://toolshed.g2.bx.psu.edu/view/yufei-luo/bwa_0_7_5 repository with the following changes: Remove .loc file, only .loc.sample should be included. Fix bwa_index.loc.sample file to contain only comments. Add suppressHeader param as in bwa_wrappers. Use $GALAXY_SLOTS environment variable when available. Add <version_command> and <help>. Remove unused import. Fix spacing and typos. Use new recommended citation. Add tool_dependencies.xml . Rename to bwa_mem. Remove definitively colorspace support. Use optparse instead of argparse since Galaxy still supports Python 2.6 . | |
| 29 | |
| 30 Development | |
| 31 ----------- | |
| 32 | |
| 33 Development is hosted at https://bitbucket.org/nsoranzo/bwa_mem . Contributions and bug reports are very welcome! |