<div dir="ltr">+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.<br><div><br></div><div>Much as I liked the "tfm" command name, "man" would be easier to discover/remember.</div><div><br></div><div>Peter</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jun 22, 2022 at 12:28 PM Kiefer, Dr. Markus <<a href="mailto:markus.kiefer@cos.uni-heidelberg.de">markus.kiefer@cos.uni-heidelberg.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Then I opt for "fmp". ;) <br>
<br>
But since emboss is packaged for the major Linux distros anyway, why not make<br>
use of the standard man pages? For Debian & friends there are autogenerated ones<br>
in place but they lack a lot of information (while tfm has a bit too much). <br>
<br>
("COPRIGHT This manual page was autogenerated from an Ajax Control Definition of<br>
the EMBOSS package.") <br>
<br>
Best, <br>
Markus <br>
<br>
Am Mittwoch, dem 22.06.2022 um 11:51 +0100 schrieb Peter Rice:<br>
> Hi Markus,<br>
> <br>
> We can make an alternative version of the tfm pages.<br>
> <br>
> All the program documentation is generated from templates as HTML and <br>
> text so a third format is not difficult.<br>
> <br>
> We use the contents of the ACD file and the input/commandline/output of <br>
> the QA tests plus the description, algorithm, author, and a few minor <br>
> details (with default values). See the doc/programs/master directory for <br>
> the templates.<br>
> <br>
> For man style we would also need another version of the -help output. <br>
> This would generate the content you need for each program.<br>
> <br>
> Then we need a new name for the program that displays them... something <br>
> with 'man' in the name. Any suggestions? 'manu' is not allowed - it <br>
> offends too many football fans. 'tfm' was one of our favourite program <br>
> names, because everyone asked what it means.<br>
> <br>
> regards,<br>
> <br>
> Peter Rice<br>
> EMBOSS team<br>
> <br>
> <br>
> On 22/06/2022 09:18, Kiefer, Dr. Markus wrote:<br>
> > Hi all.<br>
> > <br>
> > Am Mittwoch, dem 22.06.2022 um 08:06 +0000 schrieb David Bauer:<br>
> > > Hi Afif,<br>
> > > <br>
> > > There are some features in EMBOSS, which are not easy to find 😊.<br>
> > <br>
> > So this is one more for the things to be addressed list. :-)<br>
> > <br>
> > The tfm help pages aren't bad but not especially concise or user-friendly.<br>
> > That's admittedly one of the least liked tasks in development but I think<br>
> > Emboss<br>
> > could benefit a lot from a rewrite to something that more resembles<br>
> > traditional<br>
> > man pages.<br>
> > I could volunteer to lend a hand with that (if it doesn't stay the only<br>
> > hand).<br>
> > <br>
> > Best,<br>
> > Markus<br>
> > <br>
> > > If you use e.g. "transeq -help -verbose", this will then show also the<br>
> > > Associated and General qualifiers and there you will see the -filter<br>
> > > option.<br>
> > > <br>
> > > David<br>
> > > <br>
> > > -----Ursprüngliche Nachricht-----<br>
> > > Von: EMBOSS <<a href="mailto:emboss-bounces@mailman.open-bio.org" target="_blank">emboss-bounces@mailman.open-bio.org</a>> Im Auftrag von Afif<br>
> > > Elghraoui<br>
> > > Gesendet: 22 June 2022 09:55<br>
> > > An: <a href="mailto:emboss@mailman.open-bio.org" target="_blank">emboss@mailman.open-bio.org</a><br>
> > > Betreff: Re: [EMBOSS] contributing to emboss<br>
> > > <br>
> > > Wow, thank you Markus and David. I never noticed that option on the tool<br>
> > > -help<br>
> > > menus, but this changes everything :)<br>
> > > <br>
> > > thanks and regards<br>
> > > Afif<br>
> > > <br>
> > > On 6/22/22 00:52, David Bauer wrote:<br>
> > > > Hi All,<br>
> > > > <br>
> > > > If you want the -filter as default, this can be done by setting an<br>
> > > > environment variable:<br>
> > > > setenv EMBOSS_FILTER 1<br>
> > > > <br>
> > > > Best,<br>
> > > > David<br>
> > > > <br>
> > > > -----Ursprüngliche Nachricht-----<br>
> > > > Von: EMBOSS <<a href="mailto:emboss-bounces@mailman.open-bio.org" target="_blank">emboss-bounces@mailman.open-bio.org</a>> Im Auftrag von<br>
> > > > Kiefer, Dr. Markus<br>
> > > > Gesendet: 22 June 2022 09:11<br>
> > > > An: <a href="mailto:emboss@mailman.open-bio.org" target="_blank">emboss@mailman.open-bio.org</a><br>
> > > > Betreff: Re: [EMBOSS] contributing to emboss<br>
> > > > <br>
> > > > Hi Afif,<br>
> > > > <br>
> > > > do you know about the -filter option? But I agree, that should be the<br>
> > > > default.<br>
> > > > <br>
> > > > I think the retrieval functionality is in need of an overhaul. There<br>
> > > > should<br>
> > > > be an easier way to access modern Genbank for example, while e.g. SRS<br>
> > > > and<br>
> > > > GCG are much less important, meanwhile.<br>
> > > > <br>
> > > > Best,<br>
> > > > Markus<br>
> > > > <br>
> > > _______________________________________________<br>
> > > EMBOSS mailing list<br>
> > > <a href="mailto:EMBOSS@mailman.open-bio.org" target="_blank">EMBOSS@mailman.open-bio.org</a><br>
> > > <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.open-bio.org%2Fmailman%2Flistinfo%2Femboss&data=05%7C01%7C%7C3b5156e927d04f738dd508da54249205%7Cfcb2b37b5da0466b9b830014b67a7c78%7C0%7C0%7C637914813287911847%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2F2Mh5KbUeL4qgqDfHrGZxJc%2B3I9GnR0ld%2BON2%2BTWx4U%3D&reserved=0" rel="noreferrer" target="_blank">https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.open-bio.org%2Fmailman%2Flistinfo%2Femboss&data=05%7C01%7C%7C3b5156e927d04f738dd508da54249205%7Cfcb2b37b5da0466b9b830014b67a7c78%7C0%7C0%7C637914813287911847%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2F2Mh5KbUeL4qgqDfHrGZxJc%2B3I9GnR0ld%2BON2%2BTWx4U%3D&reserved=0</a><br>
> > > _______________________________________________<br>
> > > EMBOSS mailing list<br>
> > > <a href="mailto:EMBOSS@mailman.open-bio.org" target="_blank">EMBOSS@mailman.open-bio.org</a><br>
> > > <a href="https://mailman.open-bio.org/mailman/listinfo/emboss" rel="noreferrer" target="_blank">https://mailman.open-bio.org/mailman/listinfo/emboss</a><br>
> > > <br>
> > > _______________________________________________<br>
> > > EMBOSS mailing list<br>
> > > <a href="mailto:EMBOSS@mailman.open-bio.org" target="_blank">EMBOSS@mailman.open-bio.org</a><br>
> > > <a href="https://mailman.open-bio.org/mailman/listinfo/emboss" rel="noreferrer" target="_blank">https://mailman.open-bio.org/mailman/listinfo/emboss</a><br>
_______________________________________________<br>
EMBOSS mailing list<br>
<a href="mailto:EMBOSS@mailman.open-bio.org" target="_blank">EMBOSS@mailman.open-bio.org</a><br>
<a href="https://mailman.open-bio.org/mailman/listinfo/emboss" rel="noreferrer" target="_blank">https://mailman.open-bio.org/mailman/listinfo/emboss</a><br>
</blockquote></div>