Mercurial > repos > jjohnson > package_snpeff_3_3
comparison tool_dependencies.xml @ 0:a462177619be draft default tip
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| author | jjohnson |
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| date | Fri, 04 Oct 2013 09:55:46 -0400 |
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| -1:000000000000 | 0:a462177619be |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="snpEff" version="3.3"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_3_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 | |
| 21 SnpEff ( http://snpeff.sourceforge.net/ ) | |
| 22 | |
| 23 "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] | |
| 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 create 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 At this time there does not appear to be a way to edit that location during SnpEff installation. Ideally it should be relative to the galaxy genome_data_path property set in universe_wsgi.ini, e.g. genome_data_path/snpEff/data/ | |
| 34 | |
| 35 Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory: | |
| 36 ln -s genome_data_path/snpEff ~/snpEff | |
| 37 | |
| 38 </readme> | |
| 39 </package> | |
| 40 </tool_dependency> | |
| 41 |