# HG changeset patch
# User iuc
# Date 1386769587 18000
# Node ID af7ff8187d095d964f8867f2ff3cb111c528b34c

Uploaded

diff -r 000000000000 -r af7ff8187d09 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Dec 11 08:46:27 2013 -0500
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="snpEff" version="3.4">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_4_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 and SnpSift ( http://snpeff.sourceforge.net/ )
+
+SnpEff is a variant annotation and effect prediction tool by Pablo Cingolani.  
+It annotates and predicts the effects of variants on genes (such as amino acid changes).
+
+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/
+
+The location of a genome database can be set via the commandline option -dataDir.  Tools using this can generate a command line:
+java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir path_to_data_directory snpeff_database_name input.vcf
+
+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
+
+SnpEff citation:
+"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]
+
+SnpSift citation:
+"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
+
+
+        </readme>
+    </package>
+</tool_dependency>
+