# HG changeset patch
# User eganrol
# Date 1418290619 18000
# Node ID a391ca70ade5adc8db30280f03533599ba8b4637

Uploaded

diff -r 000000000000 -r a391ca70ade5 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Dec 11 04:36:59 2014 -0500
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="bowtie2" version="2.1.0">
+        <install version="1.0">
+            <actions_group>
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bowtie2/bowtie2-2.1.0-macos-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions os="linux" architecture="i386">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bowtie2/bowtie2-2.1.0-linux-i386.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions os="darwin" architecture="i386">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/bowtie2/bowtie2-2.1.0-macos-i386.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                    <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
+                    <action type="shell_command">make</action>
+                    <action type="move_file">
+                        <source>bowtie2</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>bowtie2-align</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>bowtie2-build</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>bowtie2-inspect</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme></readme>
+    </package>
+</tool_dependency>