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Use GALAXY_SLOTS for multithreading in Bowtie. Create symlinks instead of copying files. Specify in help that Bowtie is used to align the reads to the contigs. Add readme.rst .
author crs4
date Mon, 03 Mar 2014 11:28:41 -0500
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1:d180348fe9db 2:87ffe493b6c1
1 SOPRA wrapper
2 =============
3
4 Configuration
5 -------------
6
7 sopra_wpc 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 ).
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9 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.
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11 If instead you are using an older Galaxy release, you should also add a line
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13 GALAXY_SLOTS=N; export GALAXY_SLOTS
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15 (where N is the number of CPU cores allocated by the job runner for this tool) to the file
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17 <tool_dependencies_dir>/bowtie/1.0.0/crs4/sopra_wpc/<hash_string>/env.sh
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19 Version history
20 ---------------
21
22 - Release 2: Use GALAXY_SLOTS for multithreading in Bowtie. Create symlinks instead of copying files. Specify in help that Bowtie is used to align the reads to the contigs. Add readme.rst .
23 - Release 1: Depend on package_bowtie_1_0_0 .
24 - Release 0: Initial release in the Tool Shed.
25
26 Development
27 -----------
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29 Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!