Mugsy (Was: Seqan knowledge needed (Was: Help needed in C++ / seqan issue))
Hi,
I think I need to come back to this nearly one year old mail which I
seem to have left uncommented. It concerns mugsy[1]:
On Sat, 25 Apr 2015 08:52:52 +0200 Andreas Tille wrote:
> On Sat, Apr 25, 2015 at 05:30:39AM +0300, johnhommer@gmail.com wrote:
> > Here's my take on mugsy issues. I worked on a tree checked out with:
> >
> > $ svn checkout svn://svn.code.sf.net/p/mugsy/code/trunk mugsy-code
> >
> > Building with gcc-4.9.2. The version of boost I compiled it against is 1.56.
>
> OK, thanks for your patches. I'll check them soon.
>
> > I couldn't get it to link, because the authors apparently never heard
> > of autotools. Generally, those handwritten Makefile's just.. made me
> > cry.
>
> +1
>
> However, if we really want automake on these old projects we probably
> need to add it ourselves. I did so in the past for living projects and
> it was adapted upstream but I'm not sure here.
>
> Thanks a lot for your contribution - I'll come back in case of trouble
The pathces provided by Andrei are probably fine but they are patching
the original code from SVN which are basically code copies that are
removed in our source tarball anyway. The current status is:
0. The code seems to be orphaned / unmaintained since 2011.
1. Mugsy contains a *patched* version of MUMmer 3.20. I took over
those changes to the Debian MUMmer 3.23 package that sounded
sensible
2. Mugsy also contains a code copy of some files of an old seqan
version. Most of these seem to be not needed and are removed
inside get-orig-source script
Somehow the removal of the seqan files was a bad idea since when trying
to build against Debian packaged seqan I was running into several errors
which was the reason for my ask for help close to one year ago.
Since my colleagues stalled the request for the installation of Mugsy I
stopped my effort into this but the topic came up recently again. I
wonder what might be the best way to accomplish the wish to package mugsy:
1. Go with the seqan code copy?
2. Find some modern replacement that is better regarding code
maintenance as well as functionality / speed.
I can not really imagine that the last 5 years did not brought
up something better.
Any hints?
Kind regards
Andreas.
[1] git://anonscm.debian.org/debian-med/mugsy.git
--
http://fam-tille.de
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