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comparison tool_dependencies.xml @ 33:073c77ce5e94

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export PYTHONPATH during install, note python 2.7 requirement
author lparsons
date Tue, 15 Oct 2013 12:58:55 -0400
parents 580ee0c4bc4e
children ff21a055413b
comparison
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32:580ee0c4bc4e 33:073c77ce5e94
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="R" version="3.0.1"> 3 <package name="R" version="3.0.1">
4 <repository changeset_revision="7473992d1f38" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="numpy" version="1.7.1"> 6 <package name="numpy" version="1.7.1">
7 <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="rseqc" version="2.3.7"> 9 <package name="rseqc" version="2.3.7">
10 <install version="1.0"> 10 <install version="1.0">
11 <actions> 11 <actions>
12 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action> 12 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
13 <action type="shell_command">python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> 13 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
14 <action type="set_environment"> 14 <action type="set_environment">
15 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 15 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
16 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 16 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
17 </action> 17 </action>
18 </actions> 18 </actions>
19 </install> 19 </install>
20 <readme> 20 <readme>
21 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html. 21 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html.
22 Requires gcc and python. 22 Requires gcc and python 2.7.
23 </readme> 23 </readme>
24 </package> 24 </package>
25 25
26 </tool_dependency> 26 </tool_dependency>