Mercurial > repos > lparsons > htseq_count

comparison tool_dependencies.xml @ 13:30bb8acb77a4

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Updated to v0.5.4p5, use repository dependencies.
author lparsons
date Tue, 05 Nov 2013 13:02:43 -0500
parents 62a1de8c8aae
children 265ca0f35789
comparison
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12:62a1de8c8aae 13:30bb8acb77a4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="numpy" version="1.6.2"> 3
4 <package name="numpy" version="1.7.1">
5 <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
6 </package>
7
8 <package name="samtools" version="0.1.19">
9 <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
10 </package>
11
12 <package name="picard" version="1.56.0">
13 <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
14 </package>
15
16 <package name="htseq" version="0.5.4p5">
4 <install version="1.0"> 17 <install version="1.0">
5 <actions> 18 <actions>
6 <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action> 19 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action>
7 <action type="make_directory">$INSTALL_DIR/lib/python</action> 20 <!-- populate the environment variables from the dependend repos -->
8 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> 21 <action type="set_environment_for_install">
9 <action type="set_environment"> 22 <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
10 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> 23 <package name="numpy" version="1.7.1" />
11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 24 </repository>
12 </action> 25 </action>
13 </actions>
14 </install>
15 <readme>
16 </readme>
17 </package>
18
19 <package name="htseq" version="0.5.4p1">
20 <install version="1.0">
21 <actions>
22 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action>
23 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> 26 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
24 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> 27 <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 $INSTALL_DIR/bin</action> 28 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
26 <action type="set_environment"> 29 <action type="set_environment">
27 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> 30 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
28 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 31 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
29 </action> 32 </action>
30 </actions> 33 </actions>
31 </install> 34 </install>
32 <readme> 35 <readme>
33 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. 36 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
34 </readme> 37 </readme>
35 </package> 38 </package>
36 39
37 <package name="samtools" version="0.1.18">
38 <install version="1.0">
39 <actions>
40 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
41 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
42 <action type="shell_command">make</action>
43 <action type="move_file">
44 <source>samtools</source>
45 <destination>$INSTALL_DIR/bin</destination>
46 </action>
47 <action type="move_file">
48 <source>misc/maq2sam-long</source>
49 <destination>$INSTALL_DIR/bin</destination>
50 </action>
51 <action type="set_environment">
52 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
53 </action>
54 </actions>
55 </install>
56 <readme>
57 Compiling SAMtools requires the ncurses and zlib development libraries.
58 </readme>
59 </package>
60
61 <package name="picard" version="1.56.0">
62 <install version="1.0">
63 <actions>
64 <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
65 <action type="move_directory_files">
66 <source_directory>picard-tools-1.56</source_directory>
67 <destination_directory>$INSTALL_DIR/jars</destination_directory>
68 </action>
69 <action type="set_environment">
70 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
71 </action>
72 </actions>
73 </install>
74 <readme>
75 </readme>
76 </package>
77 </tool_dependency> 40 </tool_dependency>