Various data munging and loading scripts for genome database
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README.md

NAME

Modware::Loader

VERSION

version v1.10.0

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.

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

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.