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 <[email protected]> To: [email protected] <[email protected]> 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:[email protected]] > > 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 > > ________________________________ > > The information contained in this message may be confidential or legally > privileged and is intended solely for the addressee. If you have received > this message in error please delete it & notify the originator immediately. > Unauthorised use, disclosure, copying or alteration of this message is > forbidden & may be unlawful. > The contents of this e-mail are the views of the sender and do not > necessarily represent the views of the Institute. > This email and associated attachments has been checked locally for viruses > but we can accept no responsibility once it has left our systems. > Communications on Institute computers are monitored to secure the effective > operation of the systems and for other lawful purposes. > > The Pirbright Institute is a company limited by guarantee, registered in > England no. 559784. > The Institute is also a registered charity. > > -- Tim Booth <[email protected]> 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 <[email protected]> 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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/1390831812.20492.90.camel@balisaur
