Mercurial > repos > saskia-hiltemann > cgatools_v17

diff tool_dependencies.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
parents
children 977861cbcf10
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Oct 21 10:09:15 2015 -0400
@@ -0,0 +1,49 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	
+	<package name="cgatools17" version="1"> 
+		<install version="1.0">
+			<actions>
+				<action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action>
+				<action type="shell_command"> chmod a+x bin/cgatools</action>
+				<action type="move_file">
+					<source>bin/cgatools</source>
+					<destination>$INSTALL_DIR/bin</destination>
+				</action>
+				<action type="set_environment">
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+				</action>
+			</actions>
+		</install>
+		<readme>
+			Downloads and installs the cgatools binary. 
+		</readme>
+	</package>
+	
+	<package name="vcf_to_listVariants" version="1.0.0">
+		<install version="1.0">
+			<actions>
+				<!--
+				<action type="move_file">
+					<source>$REPOSITORY_INSTALL_DIR/cgatools_v17/bin/vcf_to_listVariants.py</source>
+					<destination>$INSTALL_DIR/bin/</destination>
+				</action>
+				-->
+				
+				<action type="shell_command">cp $REPOSITORY_INSTALL_DIR/cgatools_v17/tools/cgatools17/vcf_to_listVariants.py $INSTALL_DIR</action>
+				<action type="chmod">
+					<file mode="755">$INSTALL_DIR/vcf_to_listVariants.py</file>
+				</action>
+				
+				<action type="set_environment">
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/cgatools_v17/bin</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/cgatools_v17</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/bin</environment_variable>
+				</action>
+			</actions>
+		</install>
+	</package>
+	
+</tool_dependency>