Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 85:ddbaf017720a draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 19 Nov 2014 10:02:46 -0500 |
| parents | b871a8ea7d5b |
| children | c1424388f08b |
| files | README.rst tool_dependencies.xml varscan_mpileup2snp_from_bam.xml |
| diffstat | 3 files changed, 16 insertions(+), 18 deletions(-) [+] |
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--- a/README.rst Thu Nov 13 16:48:50 2014 -0500 +++ b/README.rst Wed Nov 19 10:02:46 2014 -0500 @@ -1,7 +1,7 @@ VarScan2 mpileup2snp wrapper for Galaxy ======================================= -<http://sourceforge.net/projects/varscan/> +http://sourceforge.net/projects/varscan/ This wrapper is optimized for direct access to BAM files such that the big mpileup files are not saved. @@ -11,32 +11,28 @@ * Repository-Maintainer: Youri Hoogstrate -* Repository-Development: <https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools> +* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: -<http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch> +http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch More tools by the Translational Research IT (TraIT) project can be found in the following repository: -<http://toolshed.dtls.nl/> +http://toolshed.dtls.nl/ License ------- **VarScan2**: -Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0) - -<http://sourceforge.net/directory/os:linux/license:nposl3/freshness:recently-updated/> - -<http://opensource.org/licenses/NPOSL-3.0> +Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0): http://sourceforge.net/directory/os:linux/license:nposl3/freshness:recently-updated/ http://opensource.org/licenses/NPOSL-3.0 **samtools**: -<https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE> +MIT/Expat License: https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE The MIT/Expat License @@ -73,22 +69,22 @@ **samtools-parallel-mpileup**: -<https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING> +MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING -The MIT License - + MIT License: + Copyright (c) 2008-2009 Genome Research Ltd. - + Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
--- a/tool_dependencies.xml Thu Nov 13 16:48:50 2014 -0500 +++ b/tool_dependencies.xml Wed Nov 19 10:02:46 2014 -0500 @@ -1,9 +1,8 @@ <?xml version="1.0"?> <tool_dependency> - <!-- <package name="ncurses" version="5.9"> - <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" /> </package> -->
--- a/varscan_mpileup2snp_from_bam.xml Thu Nov 13 16:48:50 2014 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Wed Nov 19 10:02:46 2014 -0500 @@ -85,6 +85,9 @@ #end if #end if + ## Make for every MPILEUP file an + ## http://en.wikipedia.org/wiki/Named_pipe + | java -Xmx64G -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar