re: Staden packaging -- [Fwd: RE: [NEBC-NBAF #14791] Staden package-gap5]
Hi Andreas,
Here's the reply from my STADEN power-user. In short, he's happy with
the package on Bio-Linux and also with the suggestion of making a
wrapper script for the binaries, so once you are done I'll pull your
changes back to BL.
Cheers,
TIM
-------- Forwarded Message --------
From: Tim Booth <tbooth@ceh.ac.uk>
To: helpdesk@nebc.nerc.ac.uk <helpdesk@nebc.nerc.ac.uk>
Subject: RE: [NEBC-NBAF #14791] Staden package-gap5
Date: Mon, 27 Jan 2014 14:05:41 +0000
Dear Jan,
Thanks for the comments. I'll leave it to Andreas but I suspect he'll
stick with the wrapper scheme I described, as this is the way I've seen
more recent packages done. For the user typing "staden stops" instead of
"staden_stops" is barely any different, and we'll add custom BASH
completion so the user can still hit tab and see the list of binaries.
Cheers,
TIM
On Mon, 2014-01-27 at 13:09 +0000, jan kim via RT wrote:
> <URL: http://nebc.nerc.ac.uk/rt-system/Ticket/Display.html?id=14791 >
>
> Dear Tim,
>
> this sounds ok to me. Regarding clashes in the namespace of binaries,
> I'd presume that prefixing binaries that have a rather common name with
> e.g. staden_ (so their names would end up staden_stops, staden_stash
> etc.) would be ok. The staden_* binaries could be implemented as wrapper
> scripts as you describe. This prefixing technique is used e.g. for the
> phylip wrappers provided by emboss (fneighbor, fprotdist etc.), and I
> think it's used in other Debian packages as well.
>
> Best regards, Jan
>
> > -----Original Message-----
> > From: Tim Booth via RT [mailto:helpdesk@nebc.nerc.ac.uk]
> > Sent: 27 January 2014 12:34
> > To: john hammond
> > Cc: jan kim
> > Subject: [NEBC-NBAF #14791] Staden package-gap5
> >
> > Dear John and Jan,
> >
> > Some time ago we corresponded regarding the packaging of GAP5 for Bio-
> > Linux. I wanted to follow up on this as we now have the opportunity
> > to push the package into the actual Debian/Ubuntu archive.
> >
> > Firstly, are you still using STADEN on Bio-Linux and are there any
> > remaining issues I still need to address?
> >
> > Secondly, Andreas, who is looking at the package for Debian, is
> > concerned about the number of generically-named binaries that are
> > dropped into /usr/bin when the normal package is installed. All
> > /usr/bin files in Debian need to be both unique and documented with a
> > manpage. He proposes the following:
> >
> > all binaries to be moved to /usr/lib/staden/bin
> >
> > gap4 pregap4 spin to be wrapper scripts in /usr/bin - ie. directly
> > runnable as normal
> >
> > a wrapper /usr/bin/staden will allow you to run other commands like
> > so:
> >
> > % staden init_exp [args]
> >
> > (as opposed to just -- % init_exp [args])
> >
> > The wrappers will all add /usr/lib/staden/bin to the PATH before
> > launching the tool so that gap[45] sees all the tools it expects when it
> > runs. This is fairly standard procedure for packages like this in
> > Debian. Does this sound like a reasonable layout for the package. Will
> > it affect any existing scripts or procedures you use?
> >
> > I think maybe tg_index and tg_view should be directly accessible under
> > /usr/bin as well. Would that make sense? It seems fine to me but then
> > I'm not an actual GAP5 user.
> >
> > (BTW, I'm still open to suggestions of a BL course if you want to
> > revisit that discussion. The last one in Colchester went really well.)
> >
> > Cheers,
> >
> > TIM
> >
> > --
> > Tim Booth
> > NERC Environmental Bioinformatics Centre
> > at CEH Wallingford
> > +44 1491 69 2705
>
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--
Tim Booth <tbooth@ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
--
Tim Booth <tbooth@ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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