[Debian-med-packaging] Bug#933937: Exonerate conflicts with biobambam

Andreas Tille andreas at an3as.eu
Mon Aug 5 11:52:29 BST 2019


On Sun, Jul 28, 2019 at 01:40:33AM +0200, Steffen Möller wrote:
> 
> Am 27.07.2019 um 20:09 schrieb Andreas Tille:
> > On Sat, Jul 27, 2019 at 07:40:45PM +0200, Steffen Möller wrote:
> > > dpkg: error processing archive
> > > /var/cache/apt/archives/exonerate_2.4.0-4_amd64.deb (--unpack):
> > >   trying to overwrite '/usr/bin/fastaexplode', which is also in package
> > > biobambam2 2.0.95-1
> > > 
> > > Grummel. Does anybody have any insights on what is going on?
> > Just guessing: You have some local package biobambam2 with a file name
> > conflict?
> 
> This one https://salsa.debian.org/med-team/biobambam2
> 
> I lack insights thought if the two are doing the very same thing or if
> this is some coincidence of some sort. We did not have too many
> conflicts without our community, yet. A stackoverflow entry points to
> the exonerate package:
> 
> https://bioinformatics.stackexchange.com/questions/7326/downloading-fasta-for-each-chromosome-of-a-complete-genome
> 
> I am tempted to put fastaexplode into a separate package . Does anybody
> by chance know if
> https://github.com/gt1/biobambam2/blob/master/src/programs/fastaexplode.cpp
> is doing the same thing? I'd otherwise contact upstream about it.

Any news about this?  We have now bug #933937 and need to care about it.
Did you contacted upstream (of both packages)? 

The fastaexplode from exonerate[1] is definitely a different codebase
than the one from biobambam2[2].  The command line interface is
definitely different when looking at the command line parsing code.  So
serving both software packages with only one pick will most probably
not work.

Kind regards

        Andreas.

[1] https://salsa.debian.org/med-team/exonerate/blob/master/src/util/fastaexplode.c
[2] https://salsa.debian.org/med-team/biobambam2/blob/master/src/programs/fastaexplode.cpp

-- 
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