[EMBOSS] contributing to emboss

[Peter Rice]

Hi Markus,

We can make an alternative version of the tfm pages.

All the program documentation is generated from templates as HTML and 
text so a third format is not difficult.

We use the contents of the ACD file and the input/commandline/output of 
the QA tests plus the description, algorithm, author, and a few minor 
details (with default values). See the doc/programs/master directory for 
the templates.

For man style we would also need another version of the -help output. 
This would generate the content you need for each program.

Then we need a new name for the program that displays them... something 
with 'man' in the name. Any suggestions? 'manu' is not allowed - it 
offends too many football fans. 'tfm' was one of our favourite program 
names, because everyone asked what it means.

regards,

Peter Rice
EMBOSS team


On 22/06/2022 09:18, Kiefer, Dr. Markus wrote:
> Hi all.
> 
> Am Mittwoch, dem 22.06.2022 um 08:06 +0000 schrieb David Bauer:
>> Hi Afif,
>>
>> There are some features in EMBOSS, which are not easy to find 😊.
> 
> So this is one more for the things to be addressed list. :-)
> 
> The tfm help pages aren't bad but not especially concise or user-friendly.
> That's admittedly one of the least liked tasks in development but I think Emboss
> could benefit a lot from a rewrite to something that more resembles traditional
> man pages.
> I could volunteer to lend a hand with that (if it doesn't stay the  only hand).
> 
> Best,
> Markus
> 
>> If you use e.g. "transeq -help -verbose", this will then show also the
>> Associated and General qualifiers and there you will see the -filter option.
>>
>> David
>>
>> -----Ursprüngliche Nachricht-----
>> Von: EMBOSS <emboss-bounces at mailman.open-bio.org> Im Auftrag von Afif
>> Elghraoui
>> Gesendet: 22 June 2022 09:55
>> An: emboss at mailman.open-bio.org
>> Betreff: Re: [EMBOSS] contributing to emboss
>>
>> Wow, thank you Markus and David. I never noticed that option on the tool -help
>> menus, but this changes everything :)
>>
>> thanks and regards
>> Afif
>>
>> On 6/22/22 00:52, David Bauer wrote:
>>> Hi All,
>>>
>>> If you want the -filter as default, this can be done by setting an
>>> environment variable:
>>> setenv EMBOSS_FILTER 1
>>>
>>> Best,
>>> David
>>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: EMBOSS <emboss-bounces at mailman.open-bio.org> Im Auftrag von
>>> Kiefer, Dr. Markus
>>> Gesendet: 22 June 2022 09:11
>>> An: emboss at mailman.open-bio.org
>>> Betreff: Re: [EMBOSS] contributing to emboss
>>>
>>> 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
>>>
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