# HG changeset patch
# User jjohnson
# Date 1377011785 14400
# Node ID 38652b57e0572716926ce40aa99d9ec59cbc27e4

Uploaded

diff -r 000000000000 -r 38652b57e057 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Aug 20 11:16:25 2013 -0400
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="bowtie" version="2.1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
+                <action type="shell_command">make BITS=64</action>
+                <action type="move_file">
+                    <source>bowtie2</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie2-build</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie2-align</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie2-inspect</source>
+                    <destination>$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>
+Program: bowtie2 (ultrafast, memory-efficient short read aligner)
+Version: 2.1.0 
+http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+
+Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
+        </readme>
+    </package>
+</tool_dependency>