Mercurial > repos > nilesh > somatic_sniper

diff tool_dependencies.xml @ 5:3b2b09506aea draft

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author nilesh
date Fri, 28 Jun 2013 16:28:56 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jun 28 16:28:56 2013 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="somatic-sniper" version="unstable">
+        <install version="1.0">
+            <actions>
+                <!-- Samtools -->
+            	<action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2</action>
+                <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
+                <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin/samtools</destination_directory>
+                </action>
+                <!-- CMake -->
+                <action type="download_by_url">http://www.cmake.org/files/v2.8/cmake-2.8.11.1.tar.gz</action>
+                <action type="shell_command">./bootstrap</action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/cmake</destination_directory>
+                <!-- Somatic Sniper -->
+                <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action>
+                <action type="download_file">https://github.com/genome/build-common/tarball/master</action>
+                <action type="shell_command">unzip master.zip</action>	
+        		<action type="shell_command">tar -xzvf master</action>
+        		<action type="shell_command">rm -rf  somatic-sniper-master/build-common/</action>
+        		<action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action>		
+                <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ &amp;&amp; make</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action> 
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        	Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
+        </readme>
+    </package>
+    
+    
+</tool_dependency>