GMODTools package preview

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GMODTools package preview

Don Gilbert

Dear colleagues,

Here is a candidate release package for GMOD Bulkfiles.

#   bulkfiles.pl -- command-line program for Bio::GMOD::Bulkfiles
#   This program generates bulk genome annotation files from a Chado genome
#   database, including Fasta, GFF, DNA, Blast indices.

If you have time to try the steps below, please let me know if your
test fails or succeeds.

It should take only a few minutes to run, and not need added software
installs if you have Postgres and a basic Perl tool set used for other
GMOD packages. If it fails at the last step, maybe for a non-obvious
reason, you could re-run with a '-debug' option and send me output to
be a big help.

  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

# if failed
  perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make -debug \
    | mail -s gmodtools-debug [hidden email]

(* It ran on my one-lung laptop in about 15 minutes; about 5 minutes
on a better computer *).

- Don
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- [hidden email]--http://marmot.bio.indiana.edu/


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Re: GMODTools package preview

Scott Cain-2
Hi Don,

I tried this out with a rice database I have that has three rice
chromosomes.  Here are the things I ran into:

* Permission denied on mkdir /usr/local/gmod//genomes

* Created ricebulk.xml and edited contents.

On what appears to be a successful execution, I've gotten this output so
far:

benicia:~/GMODTools cain$ perl -Ilib bin/bulkfiles.pl -conf ricebulk -make
Config: name = ricebulk title = Rice date = 20051129
Config: name = filesets title = Bulkfiles fileset definitions date = 20040821
Config: name = organisms date = 20051129
Config: name = featuresets title = Chado Feature mapping info date = 20040821
Config: name = ricebulk title = Rice date = 20051129
Config: name = filesets title = Bulkfiles fileset definitions date = 20040821
Config: name = organisms date = 20051129
Config: name = featuresets title = Chado Feature mapping info date = 20040821
Config: name = chadofeatsql title = Chado DB SQL date = 20051129
Config: name = chadofeatsql title = Chado DB SQL date = 20051129
Automaking feature_table files
Can't open perl script "/usr/local/gmod/tmp/remapunk": No such file or directory

It's been running for about an hour now, and I expect it may take a long
time: there are about 4 million rows in the feature table.  Do you
expect that I will run into other problems?

Thanks,
Scott


On Wed, 2005-11-30 at 12:21 -0500, Don Gilbert wrote:

> Dear colleagues,
>
> Here is a candidate release package for GMOD Bulkfiles.
>
> #   bulkfiles.pl -- command-line program for Bio::GMOD::Bulkfiles
> #   This program generates bulk genome annotation files from a Chado genome
> #   database, including Fasta, GFF, DNA, Blast indices.
>
> If you have time to try the steps below, please let me know if your
> test fails or succeeds.
>
> It should take only a few minutes to run, and not need added software
> installs if you have Postgres and a basic Perl tool set used for other
> GMOD packages. If it fails at the last step, maybe for a non-obvious
> reason, you could re-run with a '-debug' option and send me output to
> be a big help.
>
>   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
>
> # if failed
>   perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make -debug \
>     | mail -s gmodtools-debug [hidden email]
>
> (* It ran on my one-lung laptop in about 15 minutes; about 5 minutes
> on a better computer *).
>
> - Don
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- [hidden email]--http://marmot.bio.indiana.edu/
>
>
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> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         [hidden email]
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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