Mercurial > repos > nilesh > somatic_sniper

comparison tool_dependencies.xml @ 10:9d9ce3f5a383 draft

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author nilesh
date Fri, 28 Jun 2013 16:36:32 -0400
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9:2e66a79fe57f 10:9d9ce3f5a383
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="somatic-sniper" version="unstable">
4 <install version="1.0">
5 <actions>
6 <!-- CMake -->
7 <action type="download_by_url">http://www.cmake.org/files/v2.8/cmake-2.8.11.1.tar.gz</action>
8 <action type="shell_command">./bootstrap</action>
9 <action type="shell_command">make</action>
10 <action type="shell_command">make install</action>
11 <action type="move_directory_files">
12 <source_directory>.</source_directory>
13 <destination_directory>$INSTALL_DIR/cmake</destination_directory>
14 </action>
15
16 <!-- Samtools -->
17 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2</action>
18 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
19 <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile</action>
20 <action type="shell_command">make</action>
21 <action type="move_directory_files">
22 <source_directory>.</source_directory>
23 <destination_directory>$INSTALL_DIR/bin/samtools</destination_directory>
24 </action>
25
26 <!-- Somatic Sniper -->
27 <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action>
28 <action type="download_file">https://github.com/genome/build-common/tarball/master</action>
29 <action type="shell_command">unzip master.zip</action>
30 <action type="shell_command">tar -xzvf master</action>
31 <action type="shell_command">rm -rf somatic-sniper-master/build-common/</action>
32 <action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action>
33 <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ &amp;&amp; make</action>
34 <action type="move_directory_files">
35 <source_directory>bin</source_directory>
36 <destination_directory>$INSTALL_DIR/bin</destination_directory>
37 </action>
38 <action type="set_environment">
39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
40 </action>
41 </actions>
42 </install>
43 <readme>
44 Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
45 </readme>
46 </package>
47
48
49 </tool_dependency>