diff bismark_wrapper/tool_dependencies.xml @ 0:550ce7d37d4b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_wrapper/tool_dependencies.xml	Thu Oct 11 11:53:20 2012 -0400
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <!-- http://www.bioinformatics.babraham.ac.uk/projects/bismark/bismark_v0.7.7.tar.gz -->
+    <package name="bowtie2" version="2.0.0-beta7">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>bowtie2</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie2-align</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Compiling bowtie2 requires zlib and libpthread to be present on your system.
+        </readme>
+    </package>
+</tool_dependency>