Difference between revisions of "GMODTools"

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This page is a place holder for when there is a release of GMODTools, when it will be replaced with all sorts of useful information.
 
This page is a place holder for when there is a release of GMODTools, when it will be replaced with all sorts of useful information.
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[[Category:GMOD Components]]
 
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Revision as of 14:50, 5 April 2007

Description

This page is a place holder for when there is a release of GMODTools, when it will be replaced with all sorts of useful information.

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

XORT

Note that XORT offers an alternative approach to bulk uploads and downloads from a Chado database.


Downloads

Here is a candidate release package for GMODTools:

>curl -O http://eugenes.org/gmod/GMODTools/GMODTools-1.0.zip
>unzip GMODTools*.zip

If you want to try out GMODTools from CVS check out using these commands:

>cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
>cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co schema/GMODTools

These commands will create a directory named schema, with a directory named GMODTools in it. Note that you don't need to supply a password, and it may be very slow - the SourceForge anonymous CVS server is notoriously overworked.


Documentation

This package generates bulk genome annotation files from a Chado genome database, including Fasta, GFF, DNA, Blast indices.

Load a genome chado db to Postgres database:

>curl -O http://sgdlite.princeton.edu/download/sgdlite/sgdlite.sql.gz
>createdb sgdlite
>(gunzip -c sgdlite.sql.gz | psql -d sgdlite -f - ) >& log.load

Extract bulk files from database:

>cd GMODTools
>perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make

It should take only a few minutes to run.


Requirements

  • Postgres
  • Basic Perl tool set used for other GMOD packages.

Contact