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changeset 4:d58aa04f7ad6

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added zlib dependency
author nilesh
date Mon, 15 Jul 2013 13:36:57 -0500
parents 5b955fc765a3
children 02403fc450e4
files RNASeQC.xml tool_dependencies.xml
diffstat 2 files changed, 20 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/RNASeQC.xml	Fri Jul 12 15:49:28 2013 -0500
+++ b/RNASeQC.xml	Mon Jul 15 13:36:57 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="RNASeQC" name="RNASeQC">
 	<description>RNASeQC: Quality control metrics for RNA-seq data</description>
 	<requirements>
+		<requirement type="package" version="1.2.8">zlib</requirement>
 		<requirement type="package" version="0.6.2">bwa</requirement>
 		<requirement type="set_environment">RNASEQCPATH</requirement>
 	</requirements>
--- a/tool_dependencies.xml	Fri Jul 12 15:49:28 2013 -0500
+++ b/tool_dependencies.xml	Mon Jul 15 13:36:57 2013 -0500
@@ -1,9 +1,25 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	 <package name="bwa" version="0.6.2">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_bwa_0_6_2" owner="devteam" changeset_revision="8be5fbfc1548" />
+	<package name="zlib" version="1.2.8">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="zlib" owner="nilesh" changeset_revision="28f618926504" />
+    </package>
+    <package name="bwa" version="0.7.5a">
+    	<install version="1.0">
+    		<actions>
+    			<action type="set_environment_for_install">
+                    <repository changeset_revision="28f618926504" name="zlib" owner="nilesh" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="zlib" version="1.2.8" />
+                   </repository>
+                </action>
+    			<action type="download_by_url">http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.5a.tar.bz2</action>
+    			<action type="shell_command">make LIBS="-L/$ZLIB_PATH -lm -lz -lpthread"</action>
+    			<action type="set_environment">
+    				<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+    			</action>
+    		</actions>
+    	</install>
     </package>
     <set_environment version="1.0">
-        <environment_variable name="RNASEQCPATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
+        <environment_variable name="RNASEQCPATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
 </tool_dependency>