Mercurial > repos > jeremie > package_pindel_0_2_5

changeset 21:7b71d14e0f78 draft

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Uploaded
author jeremie
date Fri, 20 Jun 2014 05:05:25 -0400
parents 14facf79b652
children 2680041530ec
files tool_dependencies.xml
diffstat 1 files changed, 10 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Jun 20 04:52:48 2014 -0400
+++ b/tool_dependencies.xml	Fri Jun 20 05:05:25 2014 -0400
@@ -18,10 +18,19 @@
 				</action>
 				<action type="shell_command">unzip pindel-master.zip -d pindel</action>
 				<action type="shell_command">cd master</action> -->
-				<action type="shell_command">sed '50d' Makefile</action>
+				<!-- <action type="shell_command">sed '50d' Makefile</action> -->
 				<!-- <action type="shell_command">make Makefile.local</action> -->
+				<action type="shell_command">
+				echo "SAMTOOLS=
+				THREADS=
+				COLOUSINGBD15_TIME=60
+				COLOWOBD15_TIME=80
+				SIM1CHRVS20305_TIME=60" >> Makefile.local
+				</action>
 				<action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action>
 				<!-- <action type="shell_command">./INSTALL ~/samtools</action>  -->
+				
+				
 				<action type="move_file">
 					<source>pindel</source>
 					<destination>$INSTALL_DIR/</destination>