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1
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3
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4 <package name="rseqc" version="2.3.7">
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5 <install version = "1.0">
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6 <actions>
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7 <action type="download_by_url">https://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/rnaseqc/RNA-SeQC_v1.1.7.jar</action>
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8 <action type="shell_command">python setup.py install --root $INSTALL_DIR/lib/rseqc</action>
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9 <action type="set_environment">
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10 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/lib/python2.7/site-packages</environment_variable>
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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/lib/rseqc/usr/local/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 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
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19 </readme>
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20 </package>
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21
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22 </tool_dependency>
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