Hi Alessandra,
I think the only problem is that your chr1 line is missing a name so it
can't be found. Reformat it like this:
chr1 test region 1 500000 . . .
ID=chr1;Name=chr1
On Fri, Feb 29, 2008 at 7:01 AM, Alessandra <[EMAIL PROTECTED]>
wrote:
> Hi all,
> I would test Bio::DB::SeqFeature adaptor. I used details into webpage:
> http://www.gmod.org/wiki/index.php/GBrowse_Install_HOWTO#GFF3_Loading
> and this file as my GFF3:
> http://genomics.cribi.unipd.it/~bilardi/data/gbrowse/myfile.gff<http://genomics.cribi.unipd.it/%7Ebilardi/data/gbrowse/myfile.gff>
>
> I runned commands:
> $ mysql -u root -e "create database SF_test_db"
> $ mysql -u root -e "grant all privileges on SF_test_db.* to
> [EMAIL PROTECTED]"
> $ mysql -u root -e "grant select on SF_test_db.* to '
> apache-login'@localhost"
> $ bseqfeaturep_load.pl -u mylogin -p mypassword -d
> dbi:mysql:SF_test_db -s Bio::DB::SeqFeature -a DBI::mysql -c -f
> myfile.gff
>
> And I changed myfile.conf:
> http://genomics.cribi.unipd.it/~bilardi/data/gbrowse/myfile.conf<http://genomics.cribi.unipd.it/%7Ebilardi/data/gbrowse/myfile.conf>
> I modified myfile.conf in the head. I changed line about db_adaptor:
> db_adaptor = Bio::DB::SeqFeature::Store
> and I add line about db_args:
> -adaptor DBI::mysql
>
> This is my gbrowse page:
> http://gbrowse.cribi.unipd.it/bin/gbrowse/sf_test/
> and it has not image about tracks..
> I think that there is an error in myfile.conf or I do not add one
> basic line about Bio::DB::SeqFeature adaptor.
> I do not understand where it is the error.
> Do you know because I don't obtain this?
> With thanks in advance.
>
> Best,
> Alessandra.
> =~=~=~=~=~=~=~=~=~=~=~=~=
> CRIBI, University of Padova, Italy
> http://genomics.cribi.unipd.it
> =~=~=~=~=~=~=~=~=~=~=~=~=
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Gmod-gbrowse mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT [EMAIL PROTECTED]
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
Gmod-gbrowse mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
