# HG changeset patch
# User iuc
# Date 1460578585 14400
# Node ID 92cab2ab794826517fc645d277afc143e608dc3d

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f

diff -r 000000000000 -r 92cab2ab7948 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Apr 13 16:16:25 2016 -0400
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="hisat" version="2.0.3">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url" sha256sum="4b32770619efcc6c14dcc9c39544cd4f7946cd286776b29965347f11f00e699d">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_linux_x64.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url" sha256sum="e6bb2f06165085e6fd00408f6d1404d6875c9e58a9d3be7da966b6053789109e">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_darwin_x64.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                    <action type="download_by_url" sha256sum="b2f4aa59e000d98fc57455fd83ae69f0f50992477590ca35ce834510289d552d">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_src_all.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>