GMODTools Config files and dumping gff from chado

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GMODTools Config files and dumping gff from chado

Sofia Robb-3
Hello All,

Not sure if this is the correct mailing list, my question is about setting up the config files for GMODTools (http://gmod.org/wiki/GMODTools).

It seems from the documentation that one needs to create their own version of the sgdbulk.xml config file. Does this need to be stored in the GMODTools/conf/bulkfiles?

So far I have created my own copy of sgdbulk.xml, changed the name and many of the parameters. I see in this config that it lists an include file, site_defaults.xml. I have also edited the values in this file.

but I am getting this error when i run bulkfiles.pl

/home/gmod/trunk/GMODTools/bin/bulkfiles.pl -config=GMODTools.SmedSxl_v31.conf -format=gff,fasta -make
** Error with configuration files
Config2: file=GMODTools.SmedSxl_v31.conf; err: Died at /usr/local/share/perl/5.18.2/Bio/GMOD/Bulkfiles.pm line 525.
Died at /usr/local/share/perl/5.18.2/Bio/GMOD/Bulkfiles.pm line 525.

Can someone give me pointers on where to start with this tool? I want to use this for dumping my chado (tripal) features as gff. Is this the best tool for this? Is this something that tripal is already configured to do?

Thanks!!
Sofia



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