Mercurial > repos > fcaramia > somatic_sniper

changeset 20:6106d7e4c740 draft

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Uploaded
author fcaramia
date Wed, 19 Jun 2013 22:17:33 -0400
parents 72c57a6cd428
children 462a6a45fd77
files tool_dependencies.xml
diffstat 1 files changed, 4 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Jun 19 20:56:35 2013 -0400
+++ b/tool_dependencies.xml	Wed Jun 19 22:17:33 2013 -0400
@@ -12,20 +12,16 @@
                     <source>samtools</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
-                <action type="set_environment">
-                    <environment_variable name="SAMTOOLS_ROOT" action="set_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-                <action type="shell_command">echo $SAMTOOLS_ROOT</action>
+               
                 
-                
-                <!--action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</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">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 somatic-sniper-master/</action>
-                <action type="shell_command">make somatic-sniper-master/</action>
+                <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin somatic-sniper-master/ </action>
+                <!--action type="shell_command">make somatic-sniper-master/</action>
 	        <action type="shell_command">mv somatic-sniper-master/bin/bam-somaticsniper $INSTALL_DIR/bin</action>
                
                 <action type="set_environment">