Mercurial > repos > lparsons > htseq_count

comparison tool_dependencies.xml @ 0:3fdeebd7e710

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Initial commit
author lparsons
date Tue, 04 Sep 2012 13:45:36 -0400
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children 14e18dc9ed13
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-1:000000000000 0:3fdeebd7e710
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="htseq" version="0.5.3p9">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
7 <action type="shell_command">mkdir -p $INSTALL_DIR/lib/python</action>
8 <action type="set_environment">
9 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
10 </action>
11 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
12 <action type="set_environment">
13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
14 </action>
15 </actions>
16 </install>
17 <readme>
18 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
19 </readme>
20 </package>
21 <package name="samtools" version="0.1.18">
22 <install version="1.0">
23 <actions>
24 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
25 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
26 <action type="shell_command">make</action>
27 <action type="move_file">
28 <source>samtools</source>
29 <destination>$INSTALL_DIR/bin</destination>
30 </action>
31 <action type="move_file">
32 <source>misc/maq2sam-long</source>
33 <destination>$INSTALL_DIR/bin</destination>
34 </action>
35 <action type="set_environment">
36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
37 </action>
38 </actions>
39 </install>
40 <readme>
41 Compiling SAMtools requires the ncurses and zlib development libraries.
42 </readme>
43 </package>
44 </tool_dependency>