# HG changeset patch
# User iuc
# Date 1461102255 14400
# Node ID dc03603edd4344d86e7e6afc6431a3a3e5c62d3c

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1

diff -r 000000000000 -r dc03603edd43 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 19 17:44:15 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>