[EMBOSS] contributing to emboss

[Kiefer, Dr. Markus]

Hi Peter. 

Am Mittwoch, dem 22.06.2022 um 09:20 +0100 schrieb Peter Rice:
> Hi Markus,
> 
> In ~/.embossrc
> 
> SET EMBOSS_FILTER Y

Thanks, I wasn't aware of that. 

> Thanks also for the suggestions. What new access methods would be most 
> helpful?

Maybe an easy wrapper around NLM's e-utilities would be a good idea. Maybe even
as a predefined config in the Emboss distribution that can be readily used in a
USA, so that something like genbank:Y12345 "just works". In 6.6.0 I must admit
that I was struggling to get that to work. 

Best,
Markus 


> I did try to rescue GCG by offering to buy an open source copy but their 
> new lawyers couldn't get their head around the concept of changing the 
> license. (Even though they already changed it twice before - once as 
> University of Wisconsin, and again when they formed GCG Inc). There were 
> still some sites using it (and using EMBOSS).
> 
> regards,
> 
> Peter Rice
> EMBOSS team
> 
> On 22/06/2022 08:10, Kiefer, Dr. Markus wrote:
> > Hi Afif,
> > 
> > do you know about the -filter option? But I agree, that should be the
> > default.
> > 
> > I think the retrieval functionality is in need of an overhaul. There should
> > be
> > an easier way to access modern Genbank for example, while e.g. SRS and GCG
> > are
> > much less important, meanwhile.
> > 
> > Best,
> > Markus
> > 
> > 
> > Am Dienstag, dem 21.06.2022 um 15:33 -0700 schrieb Afif Elghraoui:
> > > Thanks for the update!
> > > 
> > > > Then the fun starts. Any suggestions for new features?
> > > 
> > > Nothing particularly fancy. What I was primarily interested in was an
> > > option
> > > for seqret to not include the genome sequence in gff output.
> > > But overall, and maybe this is too much, I would've loved for the emboss
> > > tools
> > > to be more in the unix filter style. Like if I could just
> > > 
> > >    samtools faidx gene | transeq ...
> > > 
> > > to get a translation, etc.
> > > 
> > > many thanks and regards
> > > Afif
> > > 
> > > On Tue, Jun 21, 2022 at 3:21 PM Peter Rice <ricepeterm at yahoo.co.uk> wrote:
> > > > Hi Afif,
> > > > 
> > > > Yes... it is in progress. My hopes to recover the CVS server (and all
> > > > the individual commits) came to nothing - there was no useable backup.
> > > > 
> > > > However, we do have all the old releases since the very early days, So I
> > > > have been putting them on to github. That will give us a record of every
> > > > release and a summary of all the changes made.
> > > > 
> > > > Almost there, but I have to keep up with my tranSMART development tasks
> > > > too. However, the tranSMART beta release went out today, so I will soon
> > > > have thew final rel;ease done and some free time to catch right up to
> > > > the last EMBOSS release.
> > > > 
> > > > Then the fun starts. Any suggestions for new features? I can start with
> > > > removing anything too far out of date (including some of the extra data
> > > > resources we added 10 years ago) and updating the external libraries.
> > > > 
> > > > The github repository is at https://github.com/oryzabioinformatics (but
> > > > wait for the 6.6.0 branch to appear - it is up to 6.4.0 so far, so
> > > > nearly there)
> > > > 
> > > > regards,
> > > > 
> > > > Peter Rice
> > > > 
> > > > On 21/06/2022 22:23, Afif Elghraoui wrote:
> > > > > Hello,
> > > > > I saw an old message on the -dev list that there was some migration to
> > > > > github in progress:
> > > > > https://mailman.open-bio.org/pipermail/emboss-dev/2018-January/001502.html
> > > >   
> > > > > <
> > > > https://mailman.open-bio.org/pipermail/emboss-dev/2018-January/001502.html>
> > > > > 
> > > > > Did anything ever happen with that?
> > > > > 
> > > > > thanks
> > > > > Afif
> > > > > 
> > > > > _______________________________________________
> > > > > EMBOSS mailing list
> > > > > EMBOSS at mailman.open-bio.org
> > > > > https://mailman.open-bio.org/mailman/listinfo/emboss
> > > > 
> > > > _______________________________________________
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> > > > https://mailman.open-bio.org/mailman/listinfo/emboss
> > > > 
> > > > _______________________________________________
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