Mercurial > repos > geert-vandeweyer > coverage_report
comparison tool_dependencies.xml @ 12:86df3f847a72 draft
Switched to R 3.0.2 from iuc, and moved bedtools to seperate tool_definition
| author | geert-vandeweyer |
|---|---|
| date | Thu, 20 Feb 2014 08:57:09 -0500 |
| parents | 1400dbec671f |
| children | a030e3cd3da5 |
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| 11:2936bcb2a378 | 12:86df3f847a72 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="R" version="2.11.0"> | 3 <package name="R" version="2.11.0"> |
| 4 <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> | 4 <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> |
| 5 </package> | 5 </package> |
| 6 <package name="bedtools" version="2.18.2"> | 6 <package name="bedtools" version="2.18.2"> |
| 7 <install version="1.0"> | 7 <repository changeset_revision="35905f2ae9f4" name="package_bedtools_2_18_2" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" /> |
| 8 <actions> | 8 </package> |
| 9 <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> | |
| 10 <action type="shell_command">make</action> | |
| 11 <action type="move_file"> | |
| 12 <source>bin/</source> | |
| 13 <destination>$INSTALL_DIR/bin</destination> | |
| 14 </action> | |
| 15 <action type="set_environment"> | |
| 16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 17 </action> | |
| 18 </actions> | |
| 19 </install> | |
| 20 <readme> | |
| 21 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. | |
| 22 </readme> | |
| 23 </package> | |
| 24 <package name="samtools" version="0.1.18"> | 9 <package name="samtools" version="0.1.18"> |
| 25 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> | 10 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> |
| 26 </package> | 11 </package> |
| 27 </tool_dependency> | 12 </tool_dependency> |
| 28 | 13 |