Mercurial > repos > iuc > package_snpeff_4_1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_snpeff_4_1 commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author | iuc |
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date | Tue, 07 Jun 2016 10:01:11 -0400 |
parents | cbf9c67cd731 |
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<?xml version="1.0"?> <tool_dependency> <package name="snpEff" version="4.1"> <install version="1.0"> <actions> <action type="download_by_url" sha256sum="1d5b2831c631a175b88bac57aefddea6f79588ef2ccbac8505f66e0961e54bf5">https://downloads.sourceforge.net/project/snpeff/snpEff_v4_1l_core.zip</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="shell_command">sed -i.orig -e 's;http://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action> <action type="set_environment"> <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$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 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 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: 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 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, 3:35, 2012. </readme> </package> </tool_dependency>