Mercurial > repos > fubar > htseq_bams_to_count_matrix

comparison tool_dependencies.xml @ 56:9b59cd40f20d draft

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author iuc
date Tue, 28 Apr 2015 22:56:39 -0400
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children f6211fc2f92f
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55:bf016b884c68 56:9b59cd40f20d
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="pysam" version="0.7.6">
4 <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="matplotlib" version="1.2.1">
7 <repository changeset_revision="9f3e58477115" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="htseq" version="0.5.4p3">
10 <install version="1.0">
11 <actions>
12 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
13 <action type="set_environment_for_install">
14 <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
15 <package name="pysam" version="0.7.6" />
16 </repository>
17 <repository changeset_revision="9f3e58477115" name="package_matplotlib_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="matplotlib" version="1.2.1" />
19 </repository>
20 </action>
21 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
22 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
23 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
24 <action type="set_environment">
25 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
26 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
27 </action>
28 </actions>
29 </install>
30 <readme>
31 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), pysam and the Numpy Python package.
32 Note this uses the matplotlib lite version dependent on the lite version of numpy - no atlas compilation
33 </readme>
34 </package>
35 </tool_dependency>