Mercurial > repos > fcaramia > somatic_sniper

changeset 18:b8b74ad9f841 draft

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Uploaded
author fcaramia
date Wed, 19 Jun 2013 20:46:14 -0400
parents 4fad44e7b1a2
children 72c57a6cd428
files tool_dependencies.xml
diffstat 1 files changed, 6 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Jun 19 20:28:01 2013 -0400
+++ b/tool_dependencies.xml	Wed Jun 19 20:46:14 2013 -0400
@@ -4,16 +4,14 @@
         <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_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="shell_command">export SAMTOOLS_ROOT=`pwd`</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">cd samtools-0.1.6/</action>
-                <action type="shell_command">make</action>
-                <action type="shell_command">export SAMTOOLS_ROOT=`pwd`</action>
-                <action type="shell_command">cd ..</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>