Mercurial > repos > nilesh > somatic_sniper

changeset 6:ef634ac4ed3e draft

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Deleted selected files
author nilesh
date Fri, 28 Jun 2013 16:29:46 -0400
parents 3b2b09506aea
children 32d6cdaa9691
files tool_dependencies.xml
diffstat 1 files changed, 0 insertions(+), 46 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Jun 28 16:28:56 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<?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>