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tool_dependencies.xml |
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| diff -r 000000000000 -r 35905f2ae9f4 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Feb 20 08:53:22 2014 -0500 |
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| @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <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> +</tool_dependency> |