Mercurial > repos > nilesh > somatic_sniper

comparison tool_dependencies.xml @ 30:905997f00f92 draft default tip

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author nilesh
date Mon, 08 Jul 2013 14:47:38 -0400
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29:f28a3fd3237a 30:905997f00f92
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="somatic-sniper" version="unstable">
4 <install version="1.0">
5 <actions>
6
7 <!-- Samtools -->
8 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2</action>
9 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
10 <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile</action>
11 <action type="shell_command">make</action>
12 <action type="move_directory_files">
13 <source_directory>.</source_directory>
14 <destination_directory>$INSTALL_DIR/lib/samtools</destination_directory>
15 </action>
16
17 <!-- Somatic Sniper -->
18 <action type="shell_command">git clone --recursive git://github.com/genome/somatic-sniper.git</action>
19 <action type="move_directory_files">
20 <source_directory>.</source_directory>
21 <destination_directory>$INSTALL_DIR/lib</destination_directory>
22 </action>
23 <action type="make_directory">$INSTALL_DIR/build</action>
24 <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/lib/samtools $INSTALL_DIR/lib/somatic-sniper</action>
25 <action type="shell_command">make</action>
26 <action type="move_directory_files">
27 <source_directory>.</source_directory>
28 <destination_directory>$INSTALL_DIR/build</destination_directory>
29 </action>
30 <action type="move_directory_files">
31 <source_directory>$INSTALL_DIR/build/bin</source_directory>
32 <destination_directory>$INSTALL_DIR/bin</destination_directory>
33 </action>
34 <action type="set_environment">
35 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
36 </action>
37 </actions>
38 </install>
39 <readme>
40 Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
41 </readme>
42 </package>
43
44
45 </tool_dependency>