| Next changeset 1:f776a4cff6da (2015-07-17) |
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Commit message:
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tool_dependencies.xml |
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| 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 |
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| @@ -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> + |