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 <[email protected]> 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 > > > > > [email protected] > > > > > https://mailman.open-bio.org/mailman/listinfo/emboss > > > > > > > > _______________________________________________ > > > > EMBOSS mailing list > > > > [email protected] > > > > https://mailman.open-bio.org/mailman/listinfo/emboss > > > > > > > > _______________________________________________ > > > > EMBOSS mailing list > > > > [email protected] > > > > https://mailman.open-bio.org/mailman/listinfo/emboss
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