Mercurial > repos > lparsons > htseq_count

comparison tool_dependencies.xml @ 12:62a1de8c8aae

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist
author lparsons
date Mon, 11 Mar 2013 12:44:45 -0400
parents 5d969cb56112
children 30bb8acb77a4
comparison
equal deleted inserted replaced
11:f320093f1e8e 12:62a1de8c8aae
14 </install> 14 </install>
15 <readme> 15 <readme>
16 </readme> 16 </readme>
17 </package> 17 </package>
18 18
19 <package name="htseq" version="0.5.3p9"> 19 <package name="htseq" version="0.5.4p1">
20 <install version="1.0"> 20 <install version="1.0">
21 <actions> 21 <actions>
22 <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action> 22 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action>
23 <action type="make_directory">$INSTALL_DIR/lib/python</action> 23 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
24 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> 24 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
25 <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 $INSTALL_DIR/bin</action>
25 <action type="set_environment"> 26 <action type="set_environment">
26 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> 27 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
27 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 28 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
28 </action> 29 </action>
29 </actions> 30 </actions>
30 </install> 31 </install>
31 <readme> 32 <readme>
32 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. 33 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
33 </readme> 34 </readme>
34 </package> 35 </package>
36
35 <package name="samtools" version="0.1.18"> 37 <package name="samtools" version="0.1.18">
36 <install version="1.0"> 38 <install version="1.0">
37 <actions> 39 <actions>
38 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> 40 <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> 41 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
53 </install> 55 </install>
54 <readme> 56 <readme>
55 Compiling SAMtools requires the ncurses and zlib development libraries. 57 Compiling SAMtools requires the ncurses and zlib development libraries.
56 </readme> 58 </readme>
57 </package> 59 </package>
60
58 <package name="picard" version="1.56.0"> 61 <package name="picard" version="1.56.0">
59 <install version="1.0"> 62 <install version="1.0">
60 <actions> 63 <actions>
61 <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action> 64 <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
62 <action type="move_directory_files"> 65 <action type="move_directory_files">