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

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

Don,

I finally got back around to this.  I tried the sgdlite dump from from
Princeton; here is the output:

benicia:~/GMODTools cain$  perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make Config: name = yeast title = SGD Lite 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 = yeast title = SGD Lite 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
Config: name = chadofeatconv title = Chado DB Feature info
Automaking feature_table files
Missing feature_table files; make with -featdump
Automaking dna files
Missing fff files; need -format fff
Missing dna files; need -dnadump
Missing fasta files; need -format fasta
Config: name = blastfiles title = Blast index writer
Missing formatdb: ${ARGOS_ROOT}/common/servers/blast/Bin/formatdb at lib/Bio/GMOD/Bulkfiles/BlastWriter.pm line 90.
Bulkfiles done. result=fff+gff=ok, fasta=ok, blast=ok

formatdb failing doesn't surprise me, as it isn't installed, but what
are the messages about -featdump, -format and -dnadump?  If I try adding
-dnadump to the command line, I get lots more errors (looks like one per
chromosome):

missing dumpfile /usr/local/gmod/genomes/Saccharomyces_cerevisiae/sgdlite_2005_08_23/tmp/featdump/chadofeat-chrXIII.tsv at lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm line 295.

I did get lots of stuff in the tmp directory, including chromosomes.tsv
and feature files for each chromosome.

So where should I go from here?

Thanks,
Scott


On Thu, 2005-12-01 at 00:41 -0500, Don Gilbert wrote:
> 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
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory