[EMBOSS] contributing to emboss

[Peter Rice]

Hi Markus,

The e-utilities access method is there (as "entrez"), but NCBI made some 
changes that broke access so it needs a little work.

Any URL access will have problems because EMBOSS only used http, not 
https. That is one of  the first things to fix.

These are top of the list for new/updated access methods.

regards,

Peter Rice
EMBOSS team

If you can access
On 22/06/2022 09:52, Kiefer, Dr. Markus wrote:
> 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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