Re: [Gmod-schema] Re: [GMOD-devel] GMODTools package preview

[Don G. <gil...@bi...>]

Scott,

There is an update here (same release name, new date) 
  curl -O http://eugenes.org/gmod/GMODTools/GMODTools-1.0.zip

which adds a few more validations:
dgbook%  perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make 
  ..
  ERROR: Couldn't create path /usr/local/gmod//genomes/Saccharomyces_cerevisiae: ..
  ** Need writeable data dir=/usr/local/gmod//genomes/Saccharomyces_cerevisiae
  Change configuration datadir

For those of you, like Scott, who install gmod packages according
to directions in /usr/local/gmod and have GMOD_ROOT pointing there
and can't or don't want to write data there, use this addition:

  env GMOD_ROOT=`pwd` perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make

Or edit the bulkfiles config file to point to another data root.

Even though your rice chado db is no doubt large and will take
at least a few hours to write out all features to bulk files, the first
step of finding/writing a chromosomes table is quick (<minutes).
If it fails, the rest if the job can be killed.

-- Don