0
|
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>
|