# HG changeset patch
# User iuc
# Date 1437146061 14400
# Node ID f776a4cff6da6e3f56110951b6abf7c3674ac41e
# Parent  af7ff8187d095d964f8867f2ff3cb111c528b34c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_snpeff_3_4 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty

diff -r af7ff8187d09 -r f776a4cff6da tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 11 08:46:27 2013 -0500
+++ b/tool_dependencies.xml	Fri Jul 17 11:14:21 2015 -0400
@@ -3,7 +3,7 @@
     <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="download_by_url">https://downloads.sourceforge.net/project/snpeff/snpEff_v3_4_core.zip</action>
                 <action type="move_directory_files">
                     <source_directory>.</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>
@@ -17,34 +17,30 @@
             </actions>
         </install>
         <readme>
+SnpEff and SnpSift
 
-SnpEff and SnpSift ( http://snpeff.sourceforge.net/ )
-
-SnpEff is a variant annotation and effect prediction tool by Pablo Cingolani.  
+SnpEff ( http://snpeff.sourceforge.net/ ) 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 install creates 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:
+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]
+"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 6(2):80-92, 2012
 
 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.
-
-
+"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.
         </readme>
     </package>
 </tool_dependency>
-