Mercurial > repos > lparsons > htseq_count

comparison tool_dependencies.xml @ 4:14bec14f4290

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added tool_dependencies.xml back, dependency installation requires Galaxy changeset 7621:108cda898646
author Lance Parsons <lparsons@princeton.edu>
date Tue, 11 Sep 2012 17:45:23 -0400
parents
children 971e20519fb8
comparison
equal deleted inserted replaced
3:f7a5b54a8d4f 4:14bec14f4290
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="numpy" version="1.6.2">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action>
7 <action type="make_directory">$INSTALL_DIR/lib/python</action>
8 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
9 <action type="set_environment">
10 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
12 </action>
13 </actions>
14 </install>
15 <readme>
16 </readme>
17 </package>
18
19 <package name="htseq" version="0.5.3p9">
20 <install version="1.0">
21 <actions>
22 <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
23 <action type="make_directory">$INSTALL_DIR/lib/python</action>
24 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
25 <action type="set_environment">
26 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
27 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
28 </action>
29 </actions>
30 </install>
31 <readme>
32 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
33 </readme>
34 </package>
35 <package name="samtools" version="0.1.18">
36 <install version="1.0">
37 <actions>
38 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
39 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
40 <action type="shell_command">make</action>
41 <action type="move_file">
42 <source>samtools</source>
43 <destination>$INSTALL_DIR/bin</destination>
44 </action>
45 <action type="move_file">
46 <source>misc/maq2sam-long</source>
47 <destination>$INSTALL_DIR/bin</destination>
48 </action>
49 <action type="set_environment">
50 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
51 </action>
52 </actions>
53 </install>
54 <readme>
55 Compiling SAMtools requires the ncurses and zlib development libraries.
56 </readme>
57 </package>
58 </tool_dependency>