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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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