Re: vcflib does not install scripts - missing bgziptabix
Isn't namespace pollution something that comes up when you have a
conflict? What is the chance of vcfallelicprimitives getting into a
conflict? It would have to be another VCF toolkit ;)
On Tue, May 25, 2021 at 07:41:46PM +0200, Steffen Möller wrote:
> Dear Pjotr,
>
> Am 25.05.21 um 19:18 schrieb Pjotr Prins:
> > I am looking at
> >
> > https://packages.debian.org/sid/amd64/libvcflib-tools/filelist
> >
> > and the R scripts are there. I think it is strange that many tools get
> > installed in /usr/lib/vcflib/bin/ though. Is this policy? The man
> > pages cover them all.
> >
> > wdyt?
>
> Thank you for spotting them. My hunch is that Michael wanted to avoid
> name clashess - the vcftools package for instance also has vcf-sort,
> just with a hypthen and there may be others forthcoming who then all
> fight for their position in /usr/bin.
>
> The policy is to hide away those executables that are meant for
> "internal use". So, I tend to think that this move was a bit too much on
> the side of caution.
>
> So, I think that we should come up with yet another package, called
> "vcflib" that drags in libvcflib-tools as an architecture-dependend
> dependency and that ships the scripts in /usr/bin. For the moment I am
> not sure about what to do about the binaries hidden away. I prefer
> shipping them in /usr/bin but it is Michael's package and I would want
> him to greenlight this first.
>
> Best,
> Steffen
>
> >
> > On Sun, May 23, 2021 at 05:02:01PM +0200, Pjotr Prins wrote:
> >> The vcflib installer drops the R scripts
> >>
> >> https://github.com/vcflib/vcflib/blob/master/CMakeLists.txt#L189
> >>
> >> not sure you'd want those?
> >>
> >> Pj.
> >>
> >> On Sun, May 23, 2021 at 03:47:02PM +0200, Michael R. Crusoe wrote:
> >>> Thanks for catching this, Steffen!
> >>> A bug report would be appreciated, so we don't lose track of this.
> >>> --
> >>> Michael R. Crusoe
> >>>
> >>> On Sun, May 23, 2021, 14:51 Steffen Möller <[1]steffen_moeller@gmx.de>
> >>> wrote:
> >>>
> >>> Hello,
> >>> cudaSV needs bgziptabix to be happy, which is how I became aware fo
> >>> all
> >>> the scripts in
> >>> Med/libvcflib$ ls scripts/
> >>> bed2region plotXPEHH.R vcfindelproximity
> >>> vcfnulldotslashdot vcfregionreduce_and_cut
> >>> bgziptabix vcf2bed.py vcfindels
> >>> vcfplotaltdiscrepancy.r vcfregionreduce_pipe
> >>> plotBfst.R vcf2sqlite.py vcfjoincalls
> >>> vcfplotaltdiscrepancy.sh vcfregionreduce_uncompressed
> >>> plotHaplotypes.R vcfbiallelic vcfmultiallelic
> >>> vcfplotsitediscrepancy.r vcfremovenonATGC
> >>> plotHapLrt.R vcfclearid vcfmultiway
> >>> vcfplottstv.sh vcfsnps
> >>> plotPfst.R vcfclearinfo vcfmultiwayscripts
> >>> vcfprintaltdiscrepancy.r vcfsort
> >>> plot_roc.r vcfcomplex vcfnobiallelicsnps
> >>> vcfprintaltdiscrepancy.sh vcf_strip_extra_headers
> >>> plotSmoothed.R vcffirstheader vcfnoindels
> >>> vcfqualfilter vcfvarstats
> >>> plotWCfst.R vcfgtcompare.sh vcfnosnps
> >>> vcfregionreduce
> >>> Med/libvcflib$ du -sh scripts/
> >>> 399K scripts/
> >>> being plain missing in libvcflib1 . Should there be a libvcflib-bin
> >>> package? These scripts are expected to install together with vcflib,
> >>> so
> >>> maybe having them recommended is a good idea? The vcftools package
> >>> is
> >>> something independent.
> >>> debian/rules removes *.R files, so someone on this list knows more
> >>> about
> >>> it all than me, please give some directions.
> >>> Best,
> >>> Steffen
> >>>
> >>> References
> >>>
> >>> 1. mailto:steffen_moeller@gmx.de
>
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