Re: Mugsy (Was: Seqan knowledge needed (Was: Help needed in C++ / seqan issue))
Hi Fabian,
On Tue, Apr 19, 2016 at 12:29:59PM +0200, Fabian Klötzl wrote:
> Hi Andreas,
>
> I spent the last few weeks meandering in the murky marshes of the mugsy
> source code; It is a monstrosity.
>
> Before answering to your individual points I'd like to stress that I
> *literally* spend days trying to compile mugsy with seqan 1.3 which
> comes with Ubuntu 14.04 LTS. A hundred changes in, I gave up. Most of
> the time, the compiler produces console-filling warnings, overflowing
> with templates and hiding the actual problems.
>
> Next, I built mugsyWGA with the given seqan code, which succeeded. But I
> have reason to believe the included code is not the one used to produce
> the binary in the tarball: The seqan library code produces debug output
> which does not appear in the upstream binary. (Having a library print to
> std::cerr is extremely fishy.)
>
> The "build system" is weird, to say the least. I have nothing against
> hand-written makefiles per se, but these are simply over-engineered.
> They try to be platform-agnostic, yet at the same time they include
> hard-coded paths to locations of libraries on the upstream authors
> system. Also, the seqan code is piped through a 600-lines-Python-script
> to produces "forwards". (I don't even …)
Thanks a lot for the energy you have put into this code.
> On 05.04.2016 14:45, Andreas Tille wrote:
> > 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:
> >>> 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
>
> +1 (See above)
>
> >>
> >> 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.
>
> I am unsure if this is feasible w.r.t. to the weird hacks implemented in
> the build system.
I also think that it might be a waste of time adding automake to a dead
project.
> > 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
>
> I have some extra patches for those tools, making them up to ten times
> faster. Will commit in due course.
Cool. Just ping me for sponsering.
> > 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.
>
> For porting mugsy to a newer seqan version you'd need one of the seqan
> authors from 2011 willing to waste a or two week of their lifes at
> debugging crazy error messages.
We can't probably gather a sufficient amount of money to bribe anybody
to do this horrible job.
> > 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?
>
> It has to be patched first, to provide the same functionality as the
> upstream build (see above).
Once there were patches posted to this list[2] - are you aware of these?
> > 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.
>
> My advise: drop mugsy entirely. It is just not worth it, waisting any
> more time on it. Also, according to the study [1], mugsy has inferior
> quality to other tools.
Thanks for the summary I'll foreward for further discussion.
Kind regards
Andreas.
> [1]: http://www.ncbi.nlm.nih.gov/pubmed/25273068
[2] https://lists.debian.org/debian-med/2015/04/msg00036.html
--
http://fam-tille.de
Reply to: