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annotate tool_dependencies.xml @ 1:14e18dc9ed13

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Build htseq package from source
author Lance Parsons <lparsons@princeton.edu>
date Tue, 04 Sep 2012 14:00:14 -0400
parents 3fdeebd7e710
children 265ca0f35789
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="htseq" version="0.5.3p9">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
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7 <action type="shell_command">mkdir -p $INSTALL_DIR/lib/python</action>
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8 <action type="set_environment">
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9 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
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10 </action>
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11 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py build</action>
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12 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
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13 <action type="set_environment">
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14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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15 </action>
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16 </actions>
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17 </install>
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18 <readme>
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19 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
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20 </readme>
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21 </package>
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22 <package name="samtools" version="0.1.18">
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23 <install version="1.0">
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24 <actions>
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25 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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26 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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27 <action type="shell_command">make</action>
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28 <action type="move_file">
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29 <source>samtools</source>
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30 <destination>$INSTALL_DIR/bin</destination>
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31 </action>
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32 <action type="move_file">
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33 <source>misc/maq2sam-long</source>
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34 <destination>$INSTALL_DIR/bin</destination>
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35 </action>
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36 <action type="set_environment">
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37 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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38 </action>
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39 </actions>
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40 </install>
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41 <readme>
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42 Compiling SAMtools requires the ncurses and zlib development libraries.
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43 </readme>
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44 </package>
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45 </tool_dependency>