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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
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0:af7ff8187d09 1:f776a4cff6da
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="snpEff" version="3.4"> 3 <package name="snpEff" version="3.4">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_4_core.zip</action> 6 <action type="download_by_url">https://downloads.sourceforge.net/project/snpeff/snpEff_v3_4_core.zip</action>
7 <action type="move_directory_files"> 7 <action type="move_directory_files">
8 <source_directory>.</source_directory> 8 <source_directory>.</source_directory>
9 <destination_directory>$INSTALL_DIR</destination_directory> 9 <destination_directory>$INSTALL_DIR</destination_directory>
10 </action> 10 </action>
11 <action type="set_environment"> 11 <action type="set_environment">
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable> 15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
16 </action> 16 </action>
17 </actions> 17 </actions>
18 </install> 18 </install>
19 <readme> 19 <readme>
20 SnpEff and SnpSift
20 21
21 SnpEff and SnpSift ( http://snpeff.sourceforge.net/ ) 22 SnpEff ( http://snpeff.sourceforge.net/ ) is a variant annotation and effect prediction tool by Pablo Cingolani.
22
23 SnpEff is a variant annotation and effect prediction tool by Pablo Cingolani.
24 It annotates and predicts the effects of variants on genes (such as amino acid changes). 23 It annotates and predicts the effects of variants on genes (such as amino acid changes).
25 24
26 This repository contains a tool_dependencies.xml file that downloads and installs SnpEff and SnpSift (SnpEff.jar and SnpSift.jar) 25 This repository contains a tool_dependencies.xml file that downloads and installs SnpEff and SnpSift (SnpEff.jar and SnpSift.jar)
27 26
28 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: 27 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:
29 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config ... 28 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config ...
30 29
31 The snpEff.config file is also installed, which specifies the default location for installed SnpEff genome databases: 30 The snpEff.config file is also installed, which specifies the default location for installed SnpEff genome databases:
32 data_dir = ~/snpEff/data/ 31 data_dir = ~/snpEff/data/
33 32
34 The location of a genome database can be set via the commandline option -dataDir. Tools using this can generate a command line: 33 The location of a genome database can be set via the commandline option -dataDir. Tools using this can generate a command line:
35 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 34 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
36 35
37 Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory: 36 Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory:
38 ln -s genome_data_path/snpEff ~/snpEff 37 ln -s genome_data_path/snpEff ~/snpEff
39 38
40 SnpEff citation: 39 SnpEff citation:
41 "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] 40 "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
42 41
43 SnpSift citation: 42 SnpSift citation:
44 "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. 43 "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.
45
46
47 </readme> 44 </readme>
48 </package> 45 </package>
49 </tool_dependency> 46 </tool_dependency>
50