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

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

Scott,

There is an error early in the process, maybe at sql-dump stage, from this:
Automaking feature_table files
Missing feature_table files; make with -featdump

Use the '-debug' flag to get more info, including things like SQL errors.  
  perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make -debug

Maybe there is a mismatch in Postgres db access information.  Unless you 
editted sgdbulk.xml, you are trying to use my non-standard Postgres port.

I'll change this before file release; I never use
standard ports for genome databases due to conflicts with standard uses/software.
I know this could use ENV{CHADO_DB_PORT} but with so many configs needing
special treatment for file releases, this was more precise; maybe should 
let ENV{CHADO_DB_PORT} override.

edit GMODTools/conf/bulkfiles/sgdbulk.xml
<opt
  name="sgdbulk"
  relid="5"
  date="20051129"
  ROOT="${GMOD_ROOT}/"
  datadir="data/genomes/Saccharomyces_cerevisiae"
  >
  ..
  <db
    driver="Pg"
    name="sgdlite"
    host="localhost" 
    port="7302"   << edit here; default maybe should be ${CHADO_DB_PORT} (need to test)
    user=""  << default likely should be ${CHADO_DB_USERNAME}
    password="" <<  "  ${CHADO_DB_PASSWORD}
    />

Look at files in 
genomes/Saccharomyces_cerevisiae/sgdlite_2005_08_23/tmp/featdump/

Does a chromosomes.tsv exist there and have lines like this?
If not, the first step SQL dump of chromosome features failed.
melon.% more chromosomes.tsv
chrI    1       230208  0       10      chromosome      chrI    chrI    212     species Sacch
aromyces_cerevisiae
chrII   1       813178  0       10      chromosome      chrII   chrII   507     species Sacch
aromyces_cerevisiae
...

For sgdbulk files, these are only active SQL dump files:
   1407 Nov 30 20:02 chromosomes.tsv      < 1st sql dump
7614040 Nov 30 20:02 features.tsv         < 2nd sql dump

These are produced from above two:
 126766 Nov 30 20:02 chadofeat-scerchrI.tsv
 505105 Nov 30 20:02 chadofeat-scerchrII.tsv
 ...

-=- Don
.
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gil...@in...--http://marmot.bio.indiana.edu/