Mercurial > repos > lparsons > htseq_count

diff tool_dependencies.xml @ 10:5d969cb56112

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Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
author lparsons
date Fri, 07 Dec 2012 14:35:44 -0500
parents 971e20519fb8
children 62a1de8c8aae
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Oct 26 15:57:08 2012 -0400
+++ b/tool_dependencies.xml	Fri Dec 07 14:35:44 2012 -0500
@@ -55,4 +55,20 @@
             Compiling SAMtools requires the ncurses and zlib development libraries.
         </readme>
     </package>
+    <package name="picard" version="1.56.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
+                <action type="move_directory_files">
+                    <source_directory>picard-tools-1.56</source_directory>
+                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
 </tool_dependency>