--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 19 14:58:46 2015 -0400
@@ -0,0 +1,60 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="hisat" version="0.1.5">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.5-beta-Linux_x86_64.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.5-beta-OSX_x86_64.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                  <action type="download_by_url">http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.5-beta-source.zip</action>
+                    <action type="shell_command">make</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme><![CDATA[
+HISAT is a fast and sensitive spliced alignment program.
+
+As part of HISAT, we have developed a new indexing scheme based on the
+Burrows-Wheeler transform (BWT) and the FM index, called hierarchical indexing,
+that employs two types of indexes: (1) one global FM index representing the
+whole genome, and (2) many separate local FM indexes for small regions
+collectively covering the genome. Our hierarchical index for the human genome
+(about 3 billion bp) includes ~48,000 local FM indexes, each representing a
+genomic region of ~64,000bp. As the basis for non-gapped alignment, the FM
+index is extremely fast with a low memory footprint, as demonstrated by Bowtie.
+
+In addition, HISAT provides several alignment strategies specifically designed
+for mapping different types of RNA-seq reads. All these together, HISAT enables
+extremely fast and sensitive alignment of reads, in particular those spanning
+two exons or more. As a result, HISAT is much faster >50 times than TopHat2
+with better alignment quality. Although it uses a large number of indexes, the
+memory requirement of HISAT is still modest, approximately 4.3 GB for human.
+HISAT uses the Bowtie2 implementation to handle most of the operations on the
+FM index. In addition to spliced alignment, HISAT handles reads involving
+indels and supports a paired-end alignment mode. Multiple processors can be
+used simultaneously to achieve greater alignment speed. HISAT outputs
+alignments in SAM format, enabling interoperation with a large number of other
+tools (e.g. SAMtools, GATK) that use SAM. HISAT is distributed under the GPLv3
+license, and it runs on the command line under Linux, Mac OS X and Windows.]]>
+        </readme>
+    </package>
+</tool_dependency>