[EMBOSS] contributing to emboss

[Kiefer, Dr. Markus]

Then I opt for "fmp". ;) 

But since emboss is packaged for the major Linux distros anyway, why not make
use of the standard man pages? For Debian & friends there are autogenerated ones
in place but they lack a lot of information (while tfm has a bit too much). 

("COPRIGHT This manual page was autogenerated from an Ajax Control Definition of
the EMBOSS package.") 

Best, 
Markus 

Am Mittwoch, dem 22.06.2022 um 11:51 +0100 schrieb 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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