# HG changeset patch
# User iuc
# Date 1444382245 14400
# Node ID 0f7f6f91aaee3048e5d62a53ea4582a39156b79f

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921

diff -r 000000000000 -r 0f7f6f91aaee tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 09 05:17:25 2015 -0400
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="hisat" version="2.0">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-Linux_x86_64.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-OSX_x86_64.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                  <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-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>
+                    <environment_variable action="set_to" name="HISAT2_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents the general population, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).</readme>
+    </package>
+</tool_dependency>