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. If you want to try out GMODTools in the mean time, you can get it via anonymous 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.



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

Here is a candidate release package for GMODTools .
curl -O http://eugenes.org/gmod/GMODTools/GMODTools-1.0.zip
unzip GMODTools*.zip

# 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, and not need added software
installation if you have Postgres and a basic Perl tool set used for other
GMOD packages.


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