[EMBOSS] contributing to emboss

[Peter Rice]

Hi Markus,

"As you wish" (to quote from The Princess Bride)

You can set defaults for all EMBOSS programs as environment variables, 
or in your ~/.embossrc file

For -filter

In ~/.embossrc

SET EMBOSS_FILTER Y

or define it as an environment variable.

The first input will default to stdin, the first output will default to 
stdout. You can redefine them on the command line.

For a full list of the available settings, see the output of

embossversion -full

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

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
>>>>
>>>> _______________________________________________
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>>>> EMBOSS at mailman.open-bio.org
>>>> https://mailman.open-bio.org/mailman/listinfo/emboss
>>>
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