[Gmod-help] Re: GBrowse 1.69 Plugins

[Scott Cain]

Hi Lincoln,

I think she is referring to modules written by Sheldon some time ago.
The were included in several releases (including up to 1.67 I think),
but not in 1.68 or 1.69.  For reasons that I'm not aware of, they were
removed from the MANIFEST file 20 months ago. Perhaps there is
something quite broken about them and they are no longer supported?  I
believe they were originally written to allow editing of data in a
Bio::DB::GFF database (by Artemis, I think).

I don't know anything about blat or blast plugins though.

Scott


On Sun, Nov 30, 2008 at 6:17 PM, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dave,
>
> Do you know what Blast and Blat modules Brigitte is talking about, and if so
> what the ExportFeature and ImportFeature modules are? I am not familiar with
> these modules?
>
> Lincoln
>
> On Fri, Nov 28, 2008 at 10:51 AM, "Wägele, Brigitte"
> <brigitte.waegele at helmholtz-muenchen.de> wrote:
>>
>> Dear Lincoln Stein,
>>
>> we have successfully installed GBrowse-1.69. A lot of the new stuff is
>> nice and running.
>> But with some of the plugins there are quite some difficulties. Especially
>> with Blast and Blat which need
>> the Modules ExportFeature.pm and ImportFeature.pm. Those are not included
>> in this version. After import of these
>> Modules from a previous version we still have error messages (Use of
>> uninitialized value in concatenation (.) or string at gbrowse line 320).
>> We could not find any help pages on the web and hope you can help us.
>>
>> We are looking forward to hearing from you.
>> Best regards.
>>
>> Brigitte Waegele
>> Institute for Bioinformatics and Systems Biology
>> Tel.: 089/3187-3640
>> e-Mail: brigitte.waegele at helmholtz-muenchen.de
>>
>>
>
>
>
> --
> Lincoln D. Stein
>
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>
>
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724 USA
> (516) 367-8380
> Assistant: Sandra Michelsen <michelse at cshl.edu>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research