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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bedtools" version="2.18.2">
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4 <install version="1.0">
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5 <actions>
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6 <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>
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7 <action type="shell_command">make</action>
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8 <action type="move_file">
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9 <source>bin/</source>
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10 <destination>$INSTALL_DIR/bin</destination>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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14 </action>
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15 </actions>
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16 </install>
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17 <readme>
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18 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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19 </readme>
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20 </package>
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21 </tool_dependency>
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