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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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SOPRA wrapper
=============

Configuration
-------------

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 ).

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.

If instead you are using an older Galaxy release, you should also add a line

  GALAXY_SLOTS=N; export GALAXY_SLOTS

(where N is the number of CPU cores allocated by the job runner for this tool) to the file

  <tool_dependencies_dir>/bowtie/1.0.0/crs4/sopra_wpc/<hash_string>/env.sh

Version history
---------------

- 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 .
- Release 1: Depend on package_bowtie_1_0_0 .
- Release 0: Initial release in the Tool Shed.

Development
-----------

Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!