Re: Staden packaging -- [Was: [NEBC-NBAF #14791] Staden package-gap5]
Hi,
unfortunately it has taken more time than expected but here is the
result of my try to package staden with a wrapper script:
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/staden/trunk/
Unfortunately there are some remaining issues which need to be discussed
also with Staden upstream.
1. Non-free license of tracediff/*
==================================
Probably the main issue to decide is the license of tracediff/* which is
non-free according to Debian Free Software Guidelines since it has the
"without fee" restriction:
* Copyright (c) Medical Research Council 2001. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written as part of the Staden Package at the MRC Laboratory
* of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
I see two possible solutions:
1. Upstream might drop this restriction
2. We drop the three files in tracediff/* and in case it might be
a severe restriction for Staden users we might package it up in
a separate staden-non-free package
2. Missing helpfiles
====================
The TCL interfaces og gap4, gap5, etc. are featuring a Help menu
which is refering to files /usr/share/doc/staden/manual/*.index.
For example if you want to get help in gap 4 it says:
couldn't open "/usr/share/doc/staden/manual/gap4.index": no such file or directory
I have not found such files in the source and not found a way to create
such files. However, I noticed that there are TexInfo files at
https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/doc/manual/
which might possible be turned into the needed files. Any hint to get
the help system working would be helpful.
3. Patch to simplify wrapper
============================
When the staden modules are used via wrapper it would help to apply
the following patch to the upstream code:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/debian/patches/enable_setting_stadenroot.patch?view=markup
Staden upstream developers might like to inspect all patches available
here
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/debian/patches/
anyway for future releases.
4. Problem interacting with EMBOSS databases
============================================
There seems to be some trouble accessing EMBOSS files:
$ staden create_emboss_files
no files matched glob pattern "/*.acd"
while executing
"glob $acd_dir/*.acd"
(procedure "process_files" line 3)
invoked from within
"process_files $acd_dir $acdtcl_dir"
(file "/usr/share/staden/tcl/spin_emboss/create_emboss_files.tcl" line 140)
When inspecting the source file spin_emboss/create_emboss_files.tcl I
stumbled upon the line
set acd [file dirname $dir]/../share/EMBOSS/acd
I somehow suspect that /share/EMBOSS needs to be dropped but I'd like to
let somebody more experienced with Staden and EMBOSS (and tcl) to
investigate this.
Kind regards
Andreas.
On Mon, Jan 27, 2014 at 02:10:12PM +0000, Tim Booth wrote:
> 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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