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planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
author crs4
date Thu, 31 Aug 2017 12:54:08 -0400
parents d5464c9e1723
children
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f77ce4f92b46 Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
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1 EDGE-pro wrapper
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2 ================
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4 Dependencies of EDGE-pro which need to be installed separetely
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5 --------------------------------------------------------------
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7 - Switch_ Perl module.
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9 .. _Switch: http://search.cpan.org/~rgarcia/Switch/Switch.pm
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11 Configuration
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12 -------------
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14 edge_pro 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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16 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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18 If instead you are using an older Galaxy release, you should also add a line
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20 GALAXY_SLOTS=N; export GALAXY_SLOTS
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22 (where N is the number of CPU cores allocated by the job runner for this tool) to the file
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24 <tool_dependencies_dir>/edge-pro/1.3.1/crs4/edge_pro/<hash_string>/env.sh
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26 Version history
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27 ---------------
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28
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d5464c9e1723 Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).
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29 - Release 4: Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).
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ddcbf8732706 Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like &#39;Can&#39;t exec &#34;./bowtie2-build&#34;: No such file or directory&#39;). Update Orione citation.
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30 - Release 3: Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
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bad8a51514dd Directly call edge.pl, remove edge_pro.py . Move minimun and maximum insert size params to paired library section. Update Orione citation.
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31 - Release 2: Directly call edge.pl, remove edge_pro.py . Move minimun and maximum insert size params to paired library section. Update Orione citation.
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32 - Release 1: Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
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33 - Release 0: Initial release in the Tool Shed.
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35 Development
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36 -----------
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38 Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!