Galaxy-OBO
==========

An extension of Galaxy for processing ontologies and running ontology-based analyses

Fetching the repo
-----------------

See:
https://bitbucket.org/cmungall/galaxy-obo

(Note that this is a *fork* of galaxy-dist)

You can obtain the source by getting Mercurial and typing:

hg clone https://bitbucket.org/cmungall/galaxy-obo


Setting up
----------

Follow the generic galaxy README instructions. Typically:

sh run.sh

Note that the GO galaxy setup has its own universe_wgi.ini file that
contains something like this:

tool_config_file = tool_conf_obo.xml,tool_conf_gff.xml

This can be configured to include some of the standard galaxy tools

For the BBOP setup, we use a script called staying-alive.pl that keeps
a process running. See the cron for details.
(TODO: do this using upstart or something similar)

See
https://bitbucket.org/galaxy/galaxy-central/issue/347/error-during-restart

Dependencies
------------

Note the run.sh includes a line

export PATH=$PATH:`pwd`/tools/shared/

Many tools are checked in here


tools
-----

galaxy-obo adds a number of new toolsets to the standard galaxy setup

 * obo
 * owl
 * owltools
 * annotation
 * gff


tools/obo
---------

* obo-scripts -- http://github.com/cmungall/obo-scripts

These perl scripts are standalone and require no modules. Just clone
the package and add it directory to your PATH

* owltools http://code.google.com/p/owltools/

Most ontology operations will switch to using OWLTools

* blipkit -- http://blipkit.org

Requires SWI-Prolog. No installation required, clone blipkit and add
it to your path.

tools/annotation
----------------

* GO::TermFinder

Required for term enrichment.

Standard perl module install:

  sudo cpan GO::TermFinder

* obo-scripts -- http://github.com/cmungall/obo-scripts

Required for GAF extraction

* DBI and DBD::mysql

required for extract_gaf tool [ADVANCED OPTIONS ONLY]

Making changes
--------------

$ hg commit
$ hg push

Staying in sync
---------------

Fork: https://bitbucket.org/cmungall/galaxy-obo

See:
http://mercurial.selenic.com/wiki/QuickStart

First make sure any changes you have are committed:

$ hg status
$ hg commit

Then bring in any external changes:

$ hg pull
$ hg update

Then if you had commits, push them:

$ hg push

Citing
------

See:

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy
Antezana et al
BMC Bioinformatics
http://www.biomedcentral.com/1471-2105/11/S12/S8