Mercurial > repos > iuc > package_snpeff_3_4
changeset 1:f776a4cff6da draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_snpeff_3_4 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
| author | iuc |
|---|---|
| date | Fri, 17 Jul 2015 11:14:21 -0400 |
| parents | af7ff8187d09 |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 8 insertions(+), 12 deletions(-) [+] |
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--- 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> -