[Gmod-help] bulkfiles errors

[Don Gilbert]

Barry,

I've been waiting for someone to try this Genbank submit portion of GMOD Bulkfiles,
to help them debug it.  From your error messages, I'd guess there is a configuration
file problem.  Much of Bulkfiles is tied to project-specific configurations thru
its conf/bulkfiles/ XML files.  I would guess the errors you find will be corrected
thru the config files rather than the perl code.

As a preliminary, have you successfully used Bulkfiles configured for your database to 
produce basic output like genome fasta and GFF?  THe documents included have some of that 
in examples, for synopsis:

  # load a genome chado db to Postgres database
  curl -O http://sgdlite.princeton.edu/download/sgdlite/sgdlite.sql.gz
    # I've not checked this example data for a while, but it used to work smoothly 

  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 

  To create a new genome database release configuration see
  conf/bulkfiles/bulkfiles_template.xml

-- Don Gilbert
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/