Mercurial > repos > jeremie > package_pindel_0_2_5

diff tool_dependencies.xml @ 11:aea585951b97 draft

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author jeremie
date Thu, 19 Jun 2014 10:17:34 -0400
parents ea5aad668099
children 4a11086ede4b
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Jun 19 09:50:48 2014 -0400
+++ b/tool_dependencies.xml	Thu Jun 19 10:17:34 2014 -0400
@@ -6,15 +6,19 @@
 	<package name="pindel" version="0.2.5">
 		<install version="1.0">
 			<actions>
-				<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">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">cd ..</action>
+				<action type="shell_command">ls</action>
 				<!-- <action type="move_directory_files">
 					<source_directory>.</source_directory>
 					<destination_directory>$INSTALL_DIR</destination_directory>
 				</action> -->
 				<!-- <action type="shell_command">unzip pindel-master.zip -d pindel</action>--> -->
-				<!-- <action type="shell_command">cd pindel</action> -->
+				<action type="shell_command">cd master</action>
 				<action type="shell_command">make SAMTOOLS=~/samtools</action> 
+				<action type="shell_command">./INSTALL ~/samtools</action> 
 				<action type="move_file">
 					<source>pindel</source>
 					<destination>$INSTALL_DIR/</destination>