Mercurial > repos > fcaramia > somatic_sniper

comparison tool_dependencies.xml @ 0:e81f5649bd4d draft default tip

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author fcaramia
date Thu, 20 Jun 2013 00:06:01 -0400
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-1:000000000000 0:e81f5649bd4d
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="somatic-sniper" version="unstable">
4 <install version="1.0">
5 <actions>
6
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>$INSTALL_DIR/bin/samtools</destination_directory>
14 </action>
15
16 <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action>
17 <action type="download_file">https://github.com/genome/build-common/tarball/master</action>
18 <action type="shell_command">unzip master.zip</action>
19 <action type="shell_command">tar -xzvf master</action>
20 <action type="shell_command">rm -rf somatic-sniper-master/build-common/</action>
21 <action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action>
22 <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ &amp;&amp; make</action>
23 <action type="move_directory_files">
24 <source_directory>bin</source_directory>
25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
26 </action>
27 <action type="set_environment">
28 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
29 </action>
30 </actions>
31 </install>
32 <readme>
33 Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
34 </readme>
35 </package>
36
37
38 </tool_dependency>