Mercurial > repos > nilesh > somatic_sniper

comparison tool_dependencies.xml @ 20:ca5c13b3af0e draft

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author nilesh
date Mon, 08 Jul 2013 13:43:28 -0400
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19:3a4c80abd3e5 20:ca5c13b3af0e
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>$INSTALL_DIR/lib/samtools</destination_directory>
15 </action>
16 <action type="set_environment">
17 <environment_variable name="SAMTOOLS_ROOT" action="set_to">$INSTALL_DIR/lib/samtools</environment_variable>
18 </action>
19
20 <!-- Somatic Sniper -->
21 <action type="shell_command">git clone --recursive git://github.com/genome/somatic-sniper.git</action>
22 <action type="move_directory_files">
23 <source_directory>.</source_directory>
24 <destination_directory>$INSTALL_DIR/lib</destination_directory>
25 </action>
26 <action type="make_directory">$INSTALL_DIR/build</action>
27 <action type="shell_command">cmake $INSTALL_DIR/lib/somatic-sniper</action>
28 <action type="move_directory_files">
29 <source_directory>$INSTALL_DIR/build/bin</source_directory>
30 <destination_directory>$INSTALL_DIR/bin</destination_directory>
31 </action>
32 <action type="set_environment">
33 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
34 </action>
35 </actions>
36 </install>
37 <readme>
38 Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
39 </readme>
40 </package>
41
42
43 </tool_dependency>