|
16
|
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>$INSTALL_DIR/lib/somatic-sniper</destination_directory>
|
|
|
25 </action>
|
|
|
26 <action type="make directory">$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>
|
