GBrowse plugins
|
View:
New views
4 Messages
—
Rating Filter:
Alert me
|
 |
GBrowse plugins
by Stephen Taylor-5
::
Rate this Message:
Hi,
I was wondering what is the status of GBrowse plugins? I noticed this page: http://gmod.org/wiki/GBrowse_Plugins where some are linked to. I was wondering why the others have no links. Have they stopped working? I am particularly interested in the GFFDumper plugin. Is there a place I can get the code from? Will this work on GBrowse 1.7 and GBrowse 2.0? Thanks, Steve ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: GBrowse plugins
by Scott Cain-4
::
Rate this Message:
Hi Steve,
Sorry I missed this email last week. I don't know particularly about the wiki page; I imagine Dave will have something to say about it. About the GFFDumper, it was deprecated some time ago (I don't remember when exactly) in favor of the BatchDumper, which dumps in several formats. From the code: my @FORMATS = ( 'fasta' => ['Fasta', undef], 'genbank' => ['Genbank', undef], 'embl' => ['EMBL', undef], 'gcg' => ['GCG', undef], 'raw' => ['Raw sequence', undef], 'game' => ['GAME (XML)', 'xml'], 'bsml' => ['BSML (XML)', 'xml'], 'gff' => ['GFF', undef], 'gff3' => ['GFF3', undef], If you really wanted the GFFDumper, I imagine it's in the attic of the cvs repository, but I don't know if it would still work. Scott On Sep 7, 2009, at 7:41 AM, Stephen Taylor wrote: > Hi, > > I was wondering what is the status of GBrowse plugins? I noticed this > page: > > http://gmod.org/wiki/GBrowse_Plugins > > where some are linked to. I was wondering why the others have no > links. Have they stopped working? > > I am particularly interested in the GFFDumper plugin. Is there a place > I can get the code from? Will this work on GBrowse 1.7 and GBrowse > 2.0? > > Thanks, > > Steve > > > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: GBrowse plugins
by Stephen Taylor-5
::
Rate this Message:
Hi Scott,
> > > Sorry I missed this email last week. I don't know particularly about > the wiki page; I imagine Dave will have something to say about it. > > About the GFFDumper, it was deprecated some time ago (I don't remember > when exactly) in favor of the BatchDumper, which dumps in several > formats. From the code: > > my @FORMATS = ( 'fasta' => ['Fasta', undef], > 'genbank' => ['Genbank', undef], > 'embl' => ['EMBL', undef], > 'gcg' => ['GCG', undef], > 'raw' => ['Raw sequence', undef], > 'game' => ['GAME (XML)', 'xml'], > 'bsml' => ['BSML (XML)', 'xml'], > 'gff' => ['GFF', undef], > 'gff3' => ['GFF3', undef], > > If you really wanted the GFFDumper, I imagine it's in the attic of the > cvs repository, but I don't know if it would still work. > Embarrassingly, I looked in the plugins directory and it's there! :-) Thanks for the heads up on BatchDumper. GFFToGalaxyDumper looks useful as well. Thanks, Steve > Scott > > > On Sep 7, 2009, at 7:41 AM, Stephen Taylor wrote: > >> Hi, >> >> I was wondering what is the status of GBrowse plugins? I noticed this >> page: >> >> http://gmod.org/wiki/GBrowse_Plugins >> >> where some are linked to. I was wondering why the others have no >> links. Have they stopped working? >> >> I am particularly interested in the GFFDumper plugin. Is there a >> place >> I can get the code from? Will this work on GBrowse 1.7 and GBrowse >> 2.0? >> >> Thanks, >> >> Steve >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> 30-Day >> trial. Simplify your report design, integration and deployment - and >> focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ----------------------------------------------------------------------- > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: GBrowse plugins
by Dave Clements, GMOD Help Desk
::
Rate this Message:
Hi Steve,
> Sorry I missed this email last week. I don't know particularly about > the wiki page; I imagine Dave will have something to say about it. The plugins that don't have explanatory pages just haven't had documentation created for them yet. I would like to thank Sheldon McKay for creating *all* the plugin pages that do currently exist. I encourage anyone who has worked with any of the GBrowse plugins to create a wiki page for those plugins. Your experience can help others. Thanks, Dave C. ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
| Free embeddable forum powered by Nabble | Forum Help |
