[EMBOSS] contributing to emboss

[Peter Cock]

+1 on generating "man" format documentation, putting it in the right place
at install time, and then just using the system "man" command to access it.

Much as I liked the "tfm" command name, "man" would be easier to
discover/remember.

Peter

On Wed, Jun 22, 2022 at 12:28 PM Kiefer, Dr. Markus <
markus.kiefer at cos.uni-heidelberg.de> wrote:

> 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
> > > > >
> > > > _______________________________________________
> > > > EMBOSS mailing list
> > > > EMBOSS at mailman.open-bio.org
> > > >
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