Mercurial > repos > lparsons > htseq_count

annotate tool_dependencies.xml @ 17:d5edaf8dc974 draft

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Fixed test output, added missing pysam dependency
author lparsons
date Fri, 11 Apr 2014 16:01:54 -0400
parents 227f9d3f0e32
children 3b3601a2a7c7
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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4 <package name="numpy" version="1.7.1">
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5 <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
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6 </package>
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8 <package name="samtools" version="0.1.19">
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9 <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
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10 </package>
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12 <package name="pysam" version="0.7.7">
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13 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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14 </package>
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16 <package name="htseq" version="0.6.1">
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17 <install version="1.0">
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18 <actions>
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19 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
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20 <!-- populate the environment variables from the dependend repos -->
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21 <action type="set_environment_for_install">
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22 <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
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23 <package name="numpy" version="1.7.1" />
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24 </repository>
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25 </action>
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26 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
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27 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
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28 <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 $INSTALL_DIR/bin</action>
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29 <action type="set_environment">
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30 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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31 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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32 </action>
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33 </actions>
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34 </install>
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35 <readme>
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36 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
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37 </readme>
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38 </package>
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39
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40 </tool_dependency>