GMODTools
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.
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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.