annotate tool_dependencies.xml @ 10:5d969cb56112

Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
author lparsons
date Fri, 07 Dec 2012 14:35:44 -0500
parents 971e20519fb8
children 62a1de8c8aae
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
1 <?xml version="1.0"?>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
2 <tool_dependency>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
3 <package name="numpy" version="1.6.2">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
4 <install version="1.0">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
5 <actions>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
6 <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
7 <action type="make_directory">$INSTALL_DIR/lib/python</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
8 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
9 <action type="set_environment">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
10 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
12 </action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
13 </actions>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
14 </install>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
15 <readme>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
16 </readme>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
17 </package>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
18
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
19 <package name="htseq" version="0.5.3p9">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
20 <install version="1.0">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
21 <actions>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
22 <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
23 <action type="make_directory">$INSTALL_DIR/lib/python</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
24 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
25 <action type="set_environment">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
26 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
27 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
28 </action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
29 </actions>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
30 </install>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
31 <readme>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
32 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
33 </readme>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
34 </package>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
35 <package name="samtools" version="0.1.18">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
36 <install version="1.0">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
37 <actions>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
38 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
39 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
40 <action type="shell_command">make</action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
41 <action type="move_file">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
42 <source>samtools</source>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
43 <destination>$INSTALL_DIR/bin</destination>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
44 </action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
45 <action type="move_file">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
46 <source>misc/maq2sam-long</source>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
47 <destination>$INSTALL_DIR/bin</destination>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
48 </action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
49 <action type="set_environment">
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
50 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
51 </action>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
52 </actions>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
53 </install>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
54 <readme>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
55 Compiling SAMtools requires the ncurses and zlib development libraries.
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
56 </readme>
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
57 </package>
10
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
58 <package name="picard" version="1.56.0">
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
59 <install version="1.0">
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
60 <actions>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
61 <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
62 <action type="move_directory_files">
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
63 <source_directory>picard-tools-1.56</source_directory>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
64 <destination_directory>$INSTALL_DIR/jars</destination_directory>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
65 </action>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
66 <action type="set_environment">
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
67 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
68 </action>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
69 </actions>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
70 </install>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
71 <readme>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
72 </readme>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
73 </package>
9
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 4
diff changeset
74 </tool_dependency>