Mercurial > repos > geert-vandeweyer > coverage_report
view tool_dependencies.xml @ 11:2936bcb2a378 draft
Hard Coded to use /usr/bin/Rscript instead of dependency one. Will revert when X11 issue is resolved.
author | geert-vandeweyer |
---|---|
date | Mon, 17 Feb 2014 09:49:16 -0500 |
parents | 1400dbec671f |
children | 86df3f847a72 |
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<?xml version="1.0"?> <tool_dependency> <package name="R" version="2.11.0"> <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="bedtools" version="2.18.2"> <install version="1.0"> <actions> <action type="download_by_url" target_filename="bedtools2-2.18.2.tar.gz" >https://github.com/arq5x/bedtools2/archive/v2.18.2.tar.gz</action> <action type="shell_command">make</action> <action type="move_file"> <source>bin/</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. </readme> </package> <package name="samtools" version="0.1.18"> <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>