# HG changeset patch
# User jjohnson
# Date 1380894946 14400
# Node ID a462177619be52cc6720feda0b833f9bde7a30e7

Uploaded

diff -r 000000000000 -r a462177619be tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 04 09:55:46 2013 -0400
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="snpEff" version="3.3">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_3_core.zip</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+
+SnpEff ( http://snpeff.sourceforge.net/ )
+
+"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+
+This repository contains a tool_dependencies.xml file that downloads and installs SnpEff and SnpSift (SnpEff.jar and SnpSift.jar)
+
+The install create an environment variable: SNPEFF_JAR_PATH that contains the path to the jar files.   Tools using this can generate a command line:
+java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config   ...
+
+The snpEff.config file is also installed, which specifies the default location for installed SnpEff genome databases:
+data_dir = ~/snpEff/data/
+
+At this time there does not appear to be a way to edit that location during SnpEff installation.  Ideally it should be relative to the galaxy genome_data_path property set in universe_wsgi.ini, e.g.  genome_data_path/snpEff/data/
+
+Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory:
+ln -s genome_data_path/snpEff ~/snpEff
+
+        </readme>
+    </package>
+</tool_dependency>
+