galaxy-obo / README-galaxy-obo.txt

The default branch has multiple heads


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


ONTO-ToolKit: enabling bio-ontology engineering via Galaxy
Antezana et al
BMC Bioinformatics

Fetching the repo


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

You can obtain the source by getting Mercurial and typing:

hg clone

Setting up

Follow the generic galaxy README instructions. Typically:



cp tool_conf_obo.xml tool_conf.xml

For the BBOP setup, we use a script called that keeps
a process running. See the cron for details.



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

 * obo
 * owl
 * owltools
 * annotation
 * pellet
 * gff

In future, the obo and owl toolsets will be merged. The pellet tool
will disappear, to be replaced by more general reasoner tools.


* obo-scripts --

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

* oboedit --

this is required for obo2linkfile - this tool will probably be removed
and replaced by one for owl reasoning.

You actually don't need all of oboedit - but if you follow the
standard installation then you will get the wrapper script.

* owltools

Most ontology operations will switch to using OWLTools

* blipkit --

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


* thea --
* pellet


* GO::TermFinder

Required for term enrichment.

Standard perl module install:

  sudo cpan GO::TermFinder

* obo-scripts --

Required for GAF extraction

* DBI and DBD::mysql

required for extract_gaf tool

Making changes

$ hg commit
$ hg push

Staying in sync


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
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.