Mercurial > repos > nilesh > somatic_sniper

comparison tool_dependencies.xml @ 12:4c19920a7497 draft

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author nilesh
date Fri, 28 Jun 2013 17:17:48 -0400
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11:7c44a77693f8 12:4c19920a7497
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>$INSTALL_DIR/bin/samtools</destination_directory>
15 </action>
16
17 <!-- Somatic Sniper -->
18 <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action>
19 <action type="download_file">https://github.com/genome/build-common/tarball/master</action>
20 <action type="shell_command">unzip master.zip</action>
21 <action type="shell_command">tar -xzvf master</action>
22 <action type="shell_command">rm -rf somatic-sniper-master/build-common/</action>
23 <action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action>
24 <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ &amp;&amp; make</action>
25 <action type="move_directory_files">
26 <source_directory>bin</source_directory>
27 <destination_directory>$INSTALL_DIR/bin</destination_directory>
28 </action>
29 <action type="set_environment">
30 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
31 </action>
32 </actions>
33 </install>
34 <readme>
35 Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
36 </readme>
37 </package>
38
39
40 </tool_dependency>