db_setup.pl
db_setup.pl [--options...] <UCSC database>
Options: --db <UCSC database> --path </path/to/store/database> --table [refGene|ensGene|knownGene|xenoRefGene|all] --keep --verbose --version --help
The command line flags and descriptions:
Provide the short UCSC database name for the species and version you want to use. See http://genome.ucsc.edu/FAQ/FAQreleases.html for a current list of available UCSC genomes. Examples include hg19, mm10, danRer7, sacCer3, etc.
Specify the optional path to store the SQLite database file. The default path is the ~/lib.
~/lib
Provide one or more UCSC tables to load into the database. They may be specified as comma-delimited list (no spaces) or as separate, repeated arguments. The default is refGene, ensGene, and knownGene (if available).
Keep the downloaded UCSC tables and converted GFF3 files. Default is to delete them.
Show realtime database loading progress.
Print the version number.
Display this POD documentation.
This program will simplify the task of generating an annotation database. You provide the short name of the UCSC database for the species and genome version you are interested in, and the script will automatically download gene annotation and build a Bio::DB::SeqFeature::Store database for use with BioToolBox scripts.
Timothy J. Parnell, PhD Dept of Oncological Sciences Huntsman Cancer Institute University of Utah Salt Lake City, UT, 84112
This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.
To install Bio::ToolBox, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ToolBox
CPAN shell
perl -MCPAN -e shell install Bio::ToolBox
For more information on module installation, please visit the detailed CPAN module installation guide.