Mercurial > repos > jeremie > package_pindel_0_2_5

diff tool_dependencies.xml @ 26:47817c968422 draft

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Uploaded
author jeremie
date Fri, 20 Jun 2014 10:28:26 -0400
parents 88444ff7009f
children ae37c0fd6590
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Jun 20 08:59:35 2014 -0400
+++ b/tool_dependencies.xml	Fri Jun 20 10:28:26 2014 -0400
@@ -9,6 +9,12 @@
 				<!-- <action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action> -->
 				<action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action>
 				<action type="shell_command">ls ..</action>
+				<action type="shell_command">
+					echo "$samtools
+					samtools
+					$PATH
+					$INSTALL_DIR"
+				</action>
 				<!-- <action type="shell_command">ls</action> -->
 				<!-- <action type="move_directory_files">
 					<source_directory>.</source_directory>
@@ -25,7 +31,7 @@
 				COLOWOBD15_TIME=80
 				SIM1CHRVS20305_TIME=60" > Makefile.local
 				</action>
-				<action type="shell_command">make SAMTOOLS=~/samtools THREADS=2</action>
+				<action type="shell_command">make SAMTOOLS=$samtools THREADS=2</action>
 				<action type="move_file">
 					<source>pindel</source>
 					<destination>$INSTALL_DIR/</destination>