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5
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R" version="2.11.0">
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4 <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="bedtools" version="2.18.2">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url" target_filename="bedtools-2.18.2.tar.gz" >https://github.com/arq5x/bedtools2/releases/download/v2.18.2/bedtools-2.18.2.tar.gz</action>
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10 <action type="shell_command">make</action>
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11 <action type="move_file">
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12 <source>bin/</source>
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13 <destination>$INSTALL_DIR/bin</destination>
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14 </action>
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15 <action type="set_environment">
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16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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17 </action>
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18 </actions>
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19 </install>
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20 <readme>
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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.
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22 </readme>
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23 </package>
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24 <package name="samtools" version="0.1.18">
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25 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
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26 </package>
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27 </tool_dependency>
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28
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