Mercurial > repos > lparsons > htseq_count

annotate tool_dependencies.xml @ 16:227f9d3f0e32 draft

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Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions
author lparsons
date Fri, 11 Apr 2014 15:05:28 -0400
parents 265ca0f35789
children d5edaf8dc974
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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="htseq" version="0.6.1">
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13 <install version="1.0">
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14 <actions>
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15 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
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16 <!-- populate the environment variables from the dependend repos -->
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17 <action type="set_environment_for_install">
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18 <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
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19 <package name="numpy" version="1.7.1" />
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20 </repository>
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21 </action>
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22 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
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23 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
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24 <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 $INSTALL_DIR/bin</action>
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25 <action type="set_environment">
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26 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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27 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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28 </action>
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29 </actions>
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30 </install>
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31 <readme>
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32 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
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33 </readme>
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34 </package>
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36 </tool_dependency>