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 (

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

/home/gmod/trunk/GMODTools/bin/ -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/ line 525.
Died at /usr/local/share/perl/5.18.2/Bio/GMOD/ 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?


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