Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 2:ede8c645ed22

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Uploaded
author yhoogstrate
date Tue, 17 Dec 2013 04:52:45 -0500
parents d0cd5668ec6b
children 436d89c21432
files tool_dependencies.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Dec 17 04:41:18 2013 -0500
+++ b/tool_dependencies.xml	Tue Dec 17 04:52:45 2013 -0500
@@ -3,9 +3,9 @@
 	<package name="samtools-mpileup-parallel" version="1.0.19">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel &amp;&amp; cd samtools-mpileup-parallel &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-mpileup-parallel &amp;&amp; ls -als &amp;&amp; cd .. &amp;&amp; ls -als</action>
+				<action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel &amp;&amp; cd samtools-mpileup-parallel &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../ &amp;&amp; ls -als &amp;&amp; cd .. &amp;&amp; ls -als</action>
 				<action type="move_file">
-					<source>bin/samtools</source>
+					<source>samtools</source>
 					<destination>$INSTALL_DIR/bin</destination>
 				</action>
 				<action type="set_environment">
@@ -21,7 +21,7 @@
 	<package name="VarScan" version="2.3.6">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">wget http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
+				<action type="shell_command">wget http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar &amp;&amp; pwd &amp;&amp; ls -als</action>
 				<action type="move_file">
 					<source>VarScan.v2.3.6.jar</source>
 					<destination>$INSTALL_DIR/bin</destination>