# HG changeset patch
# User devteam
# Date 1442425119 14400
# Node ID ee153209837a1d92835a191f8e3549287fa608cc

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be

diff -r 000000000000 -r ee153209837a tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 16 13:38:39 2015 -0400
@@ -0,0 +1,35 @@
+<?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>
+                </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>