Mercurial > repos > fcaramia > somatic_sniper

diff tool_dependencies.xml @ 15:305c0316b77c draft

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Uploaded
author fcaramia
date Wed, 19 Jun 2013 20:21:07 -0400
parents 3c81335a4534
children 17b9adf1f961
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Jun 19 20:20:53 2013 -0400
+++ b/tool_dependencies.xml	Wed Jun 19 20:21:07 2013 -0400
@@ -24,8 +24,15 @@
     <package name="somatic-sniper" version="unstable">
         <install version="1.0">
             <actions>
+            
+            	<action type="download_file">http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2</action>
                 <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">tar -xjf samtools-0.1.6.tar.bz2</action>	
+                <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' samtools-0.1.6/Makefile</action>
+                <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' samtools-0.1.6/Makefile</action>
+                <action type="shell_command">samtools-0.1.6/make</action>
+                <action type="shell_command">export SAMTOOLS_ROOT=`pwd`/samtools-0.1.6/</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>