Mercurial > repos > nml > package_python_3_4_pysam_0_8_3

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_pysam_0_8_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
author nml
date Thu, 07 Jul 2016 09:56:33 -0400
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-1:000000000000 0:085a17b297b1
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="python" version="3.4">
4 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="pysam" version="0.8.3">
7 <install version="1.0">
8 <actions>
9 <action type="download_by_url">https://depot.galaxyproject.org/software/pysam/pysam_0.8.3_src_all.tar.gz</action>
10 <action type="set_environment_for_install">
11 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
12 <package name="python" version="3.4" />
13 </repository>
14 </action>
15 <action type="make_directory">$INSTALL_DIR/lib/python</action>
16 <action type="shell_command">
17 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
18 python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
19 </action>
20 <action type="set_environment">
21 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
22 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
23 <environment_variable action="set_to" name="PYTHONPATH_PYSAM">$INSTALL_DIR/lib/python</environment_variable>
24 <environment_variable action="set_to" name="PATH_PYSAM">$INSTALL_DIR/bin</environment_variable>
25 <environment_variable action="set_to" name="PYSAM_ROOT_DIR">$INSTALL_DIR</environment_variable>
26 </action>
27 </actions>
28 </install>
29 <readme>
30 Installation of pysam, pyrex and python are required. The installation can be accessed via PYSAM_PATH.
31 </readme>
32 </package>
33 </tool_dependency>