# HG changeset patch
# User devteam
# Date 1390832703 18000
# Node ID 0fea0c8cc6cf69e893513e92622826d524c09db8

Imported from capsule None

diff -r 000000000000 -r 0fea0c8cc6cf tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 27 09:25:03 2014 -0500
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="tophat" version="1.4.0">
+      <install version="1.0">
+          <actions_group>
+              <actions architecture="x86_64" os="linux">
+                  <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/tophat/tophat-1.4.0.Linux_x86_64.tar.gz</action>
+                    <action type="move_directory_files">
+                      <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                  <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/tophat/tophat-1.4.0.OSX_x86_64.tar.gz</action>
+                    <action type="move_directory_files">
+                      <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                  <package name="samtools" version="0.1.18">
+                      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <action type="download_by_url">http://tophat.cbcb.umd.edu/downloads/tophat-1.4.0.tar.gz</action>
+                    <action type="set_environment_for_install">
+                      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </action>
+                    <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-bam=$BAM_ROOT</action>
+                    <action type="shell_command">make &amp;&amp; make install</action>
+                </actions>
+                <action type="set_environment">
+                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme />
+    </package>
+</tool_dependency>