Mercurial > repos > fcaramia > somatic_sniper

changeset 9:e54d338a2842 draft

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Uploaded
author fcaramia
date Wed, 19 Jun 2013 03:27:10 -0400
parents e22f923f4899
children 6d709235e747
files tool_dependencies.xml
diffstat 1 files changed, 14 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Jun 19 02:51:19 2013 -0400
+++ b/tool_dependencies.xml	Wed Jun 19 03:27:10 2013 -0400
@@ -24,12 +24,21 @@
     <package name="somatic-sniper" version="unstable">
         <install version="1.0">
             <actions>
-                
-                <action type="shell_command">git clone --recursive git://github.com/genome/somatic-sniper.git</action>
-                <action type="shell_command">cmake</action>
-                <action type="shell_command">make</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 -xzf master</action>
+		<action type="shell_command">rm -rf  somatic-sniper-master/build-common</action>
+		<action type="move_directory_files">
+                    <source_directory>genome-build-common-077bd57</source_directory>
+                    <destination_directory>somatic-sniper-master/build-common</destination_directory>
+                </action>
+		
+
+                <action type="shell_command">cmake somatic-sniper-master/</action>
+                <action type="shell_command">make somatic-sniper-master/</action>
                 <action type="move_file">
-                    <source>bin/bam-somaticsniper</source>
+                    <source>somatic-sniper-master/bin/bam-somaticsniper</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
                 <action type="set_environment">