Hi John
Artemis 11 is the recommended version to be using. One way to diagnose this
is to open the Artemis log window if you can. This is under the Options menu
in the startup window. From this hopefully you will see what queries it is
running.
It may be not finding your sequence features. To build the list of organisms
with sequences with residues it will run something like this:
SELECT DISTINCT ON( feature.organism_id ) organism.organism_id
AS organismId, abbreviation, genus, species, common_name
AS commonName, comment
FROM feature join organism using (organism_id) join cvterm on
feature.type_id = cvterm.cvterm_id WHERE residues notnull AND residues !=
'' AND ( cvterm.name LIKE '%chromosome%' OR cvterm.name LIKE
'%sequence%' OR cvterm.name IN ('supercontig', 'ultra_scaffold',
'golden_path_region', 'contig') ) ;
Regards
Tim
On 10/6/09 9:56 PM, "John Martin" <jmar...@watson.wustl.edu> wrote:
> I'm a novice user of both chado & artemis, and I'm having trouble
> getting artemis to see a chado db that I've recently setup. I've tried
> using both artemis release 10 & 11, and am having similar problems with
> both.
>
> I'm fairly confident that I have the chado db set correctly, since I'm
> able to view it under gbrowse using the host/port/database/user/pwd that
> I have set. Then I've been calling up the artemis gui using this
> command line:
>
> ./art -Dchado="vm22:5432/chado_dev?chuser" -Dibatis
> -Djdbc.drivers=org.postgresql.Driver
>
> Under release 10.0, the gui opens and then I get a password dialogue
> box. When I type in the password, the box goes away and returns in
> about 5 seconds. Its not giving me errors, the box just comes back and
> asks me to enter the password again.
>
> Under release 11.0, the gui opens, and I am only asked to enter the
> password once. Then I am able to use the gui, but the file & database
> management window only displays the root level directory (just the
> folder icon, no name). When I click on that folder artemis just goes
> into a 'working' state (with the little clock icon turning) and never
> returns. I've let it run for over an hour and it just keeps churning.
>
>
> Can anyone advise me on what I might be doing wrong?
>
> Thanks,
> John Martin
>
>
>
> _______________________________________________
> Artemis-users mailing list
> Artemis-users@sanger.ac.uk
> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
_______________________________________________
Artemis-users mailing list
Artemis-users@sanger.ac.uk
http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
