|
5
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <package name="somatic-sniper" version="unstable">
|
|
|
4 <install version="1.0">
|
|
|
5 <actions>
|
|
|
6 <!-- Samtools -->
|
|
|
7 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2</action>
|
|
|
8 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
|
|
|
9 <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile</action>
|
|
|
10 <action type="shell_command">make</action>
|
|
|
11 <action type="move_directory_files">
|
|
|
12 <source_directory>.</source_directory>
|
|
|
13 <destination_directory>$INSTALL_DIR/bin/samtools</destination_directory>
|
|
|
14 </action>
|
|
|
15 <!-- CMake -->
|
|
|
16 <action type="download_by_url">http://www.cmake.org/files/v2.8/cmake-2.8.11.1.tar.gz</action>
|
|
|
17 <action type="shell_command">./bootstrap</action>
|
|
|
18 <action type="shell_command">make</action>
|
|
|
19 <action type="shell_command">make install</action>
|
|
|
20 <action type="move_directory_files">
|
|
|
21 <source_directory>.</source_directory>
|
|
|
22 <destination_directory>$INSTALL_DIR/cmake</destination_directory>
|
|
|
23 <!-- Somatic Sniper -->
|
|
|
24 <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action>
|
|
|
25 <action type="download_file">https://github.com/genome/build-common/tarball/master</action>
|
|
|
26 <action type="shell_command">unzip master.zip</action>
|
|
|
27 <action type="shell_command">tar -xzvf master</action>
|
|
|
28 <action type="shell_command">rm -rf somatic-sniper-master/build-common/</action>
|
|
|
29 <action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action>
|
|
|
30 <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ && make</action>
|
|
|
31 <action type="move_directory_files">
|
|
|
32 <source_directory>bin</source_directory>
|
|
|
33 <destination_directory>$INSTALL_DIR/bin</destination_directory>
|
|
|
34 </action>
|
|
|
35 <action type="set_environment">
|
|
|
36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
|
|
|
37 </action>
|
|
|
38 </actions>
|
|
|
39 </install>
|
|
|
40 <readme>
|
|
|
41 Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
|
|
|
42 </readme>
|
|
|
43 </package>
|
|
|
44
|
|
|
45
|
|
|
46 </tool_dependency>
|
