NAME

Modware::Loader

VERSION

version v1.10.5

DESCRIPTION

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.

NAME

Modware::Loader - Command line apps for Chado relational database

INSTALLATION

Install using cpanm is highly recommended. Use a latest version of cpanm, at least 1.6 is needed.

Latest release

cpanm -n  git://github.com/dictyBase/Modware-Loader.git

Any particular release

Download the respective tarballs from their release pages in github and invoke cpanm on them locally.

• Modware-Loader release pages

Using Build.PL, cpan and friends

Just follow the instuctions in the INSTALL file.

Using docker

Use any particular tag from docker hub

$_> docker run --rm dictybase/modware-loader:1.8 <cmd>

Build Status

Documentation

Run any one of the following command

• modware-export
• modware-load
• modware-transform
• modware-update

Then follow the instructions to run any of the subcommand. Invoking the subcommand will display further help which is more or less self-explanatory.

Quick example

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

Done.

Tutorials/Blog posts

• Exporting annotations
• Converting tblastn alignments to GFF3 format
• Design pattern of chado loader

Automated release and docker build

This is only meant for developers. The automated process is done through `Makefile`.

Prerequisites

• Docker
• curl
• jq
• Github personal access token . Store it in `~/.github-release` file.

Then bump the version in `dist.ini` file and run the command

$_> make release && make gh-release

AUTHOR

Siddhartha Basu biosidd@gmail.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.