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

[Scott C. <ca...@cs...>]

It seems that result files from earlier failures where somehow poisoning
the stew, because when I delete the output directory and reran,
everything worked fine.  I imagine you want to keep those directories to
work as a cache, but you might want a flag (or already have one) to do
the equiv of a make clean.

On Fri, 2005-12-09 at 13:30 -0500, Don Gilbert wrote:
> 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/
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory