Mercurial > repos > jjohnson > package_snpeff_3_6
comparison tool_dependencies.xml @ 0:849895b37940 draft default tip
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author | jjohnson |
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date | Tue, 24 Jun 2014 17:21:45 -0400 |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="snpEff" version="3.6"> | |
4 <install version="1.0"> | |
5 <actions> | |
6 <action type="download_by_url">https://downloads.sourceforge.net/project/snpeff/snpEff_v3_6_core.zip</action> | |
7 <action type="move_directory_files"> | |
8 <source_directory>.</source_directory> | |
9 <destination_directory>$INSTALL_DIR</destination_directory> | |
10 </action> | |
11 <action type="set_environment"> | |
12 <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> | |
13 </action> | |
14 <action type="set_environment"> | |
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable> | |
16 </action> | |
17 </actions> | |
18 </install> | |
19 <readme> | |
20 SnpEff and SnpSift | |
21 | |
22 SnpEff ( http://snpeff.sourceforge.net/ ) is a variant annotation and effect prediction tool by Pablo Cingolani. | |
23 It annotates and predicts the effects of variants on genes (such as amino acid changes). | |
24 | |
25 This repository contains a tool_dependencies.xml file that downloads and installs SnpEff and SnpSift (SnpEff.jar and SnpSift.jar) | |
26 | |
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: | |
28 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config ... | |
29 | |
30 The snpEff.config file is also installed, which specifies the default location for installed SnpEff genome databases: | |
31 data_dir = ~/snpEff/data/ | |
32 | |
33 The location of a genome database can be set via the commandline option -dataDir. Tools using this can generate a command line: | |
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 | |
35 | |
36 Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory: | |
37 ln -s genome_data_path/snpEff ~/snpEff | |
38 | |
39 SnpEff citation: | |
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 | |
41 | |
42 SnpSift citation: | |
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. | |
44 </readme> | |
45 </package> | |
46 </tool_dependency> |