Difference between revisions of "GMODTools"
From GMOD
(New page: 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, yo...) |
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| + | ==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. If you want to try out GMODTools in the mean time, you can get it via anonymous cvs check out using these commands: | 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 login |
| − | cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co schema/GMODTools | + | >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 | + | 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<br /> database, including Fasta, GFF, DNA, Blast indices. | ||
| + | Here is a candidate release package for [http://eugenes.org/gmod/GMODTools/ 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 | + | 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. |
| − | + | [[Category:GMOD Components]] | |
Revision as of 18:32, 11 February 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. 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.
Documentation
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.
