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annotate readme.rst @ 2:bc4451edb703 draft

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Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.
author crs4
date Mon, 27 Oct 2014 14:11:57 -0400
parents 93fa7ecb5292
children
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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1 SSPACE wrapper
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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2 ==============
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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4 Configuration
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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5 -------------
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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7 sspace 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 ).
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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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.
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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11 If instead you are using an older Galaxy release, you should also add a line
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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13 GALAXY_SLOTS=N; export GALAXY_SLOTS
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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15 (where N is the number of CPU cores allocated by the job runner for this tool) to the file
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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bc4451edb703 Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.
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17 <tool_dependencies_dir>/sspace/2.1/crs4/sspace/<hash_string>/env.sh
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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19 Version history
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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20 ---------------
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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bc4451edb703 Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.
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22 - Release 2: Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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23 - Release 1: Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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24 - Release 0: Initial release in the Tool Shed.
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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26 Development
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27 -----------
93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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93fa7ecb5292 Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
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29 Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!