Re: vcflib does not install scripts - missing bgziptabix
Dear Steffen,
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?
Pj.
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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