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43
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="pysam" version="0.7.6">
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49
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4 <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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43
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5 </package>
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47
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6 <package name="matplotlib" version="1.2.1">
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49
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7 <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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43
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8 </package>
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9 <package name="htseq" version="0.5.4p3">
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10 <install version="1.0">
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11 <actions>
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49
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12 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
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43
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13 <action type="set_environment_for_install">
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49
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14 <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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43
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15 <package name="pysam" version="0.7.6" />
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16 </repository>
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49
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17 <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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47
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18 <package name="matplotlib" version="1.2.1" />
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43
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19 </repository>
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20 </action>
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48
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21 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
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22 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
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43
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23 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
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24 <action type="set_environment">
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25 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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26 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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27 </action>
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28 </actions>
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29 </install>
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30 <readme>
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31 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), pysam and the Numpy Python package.
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32 Note this uses the matplotlib lite version dependent on the lite version of numpy - no atlas compilation
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33 </readme>
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34 </package>
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35 </tool_dependency>
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