Chado is an open-source modular database schema for biological data. This distribution provides MooseX::App::Cmd based command line applications to import and export biological data from Chado database.
Modware::Loader - Command line apps for Chado relational database
You need to install 2/3 dependencies from github, rest of them would be pulled from CPAN as needed. Install using cpanm is highly recommended. Use a latest version of cpanm, at least 1.6 is needed.
cpanm -n git://github.com/dictyBase/Modware-Loader.git
If you install without (-n/notest flag) then install Test::Chado before you install BioPortal-Webservice.
Any particular release
Download the respective tarballs from their release pages in github and invoke cpanm on them locally.
Using Build.PL, cpan and friends
Just follow the instuctions in the INSTALL file.
Run any one of the following command
Then follow the instructions to run any of the subcommand. Invoking the subcommand will display further help which is more or less self-explanatory.
Run one of the command
$_> modware-load Available commands: commands: list the application's commands help: display a command's help screen adhocobo2chado: Load an adhoc ontology in chado database obo2chado: Load ontology from obo flat file to chado database oboclosure2chado: Populate cvtermpath in chado database bioportalobo2chado: Load ontology from NCBO bioportal to chado database dictygaf2chado: Load GO annotations from GAF file to chado database dropontofromchado: Drop ontology from chado database (use sparingly) gb2chado: Populate oracle chado database from genbank file gbassembly2chado: Load genome assembly from genbank to oracle chado database
Run one subcommand
$_> modware-load obo2chado modware-load obo2chado [-?chilpu] [long options...] -i --input Name of the obo file --dry_run Dry run do not save anything in database -h -? --usage --help Prints this usage information. --pg_schema Name of postgresql schema where the ontology will be loaded, default is public, obviously ignored for other backend --sqllib Path to sql library in INI format, by default picked up from the shared lib folder. Mostly a developer option. --attr --attribute Additional database attribute --pass -p --password database password
Execute the subcommand
$_> modware-load obo2chado --dsn 'dbi:Pg:database=mychado' -u tucker -p tucker -i go.obo
Siddhartha Basu email@example.com
COPYRIGHT AND LICENSE
This software is copyright (c) 2011 by Siddhartha Basu.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.