Re: vcflib does not install scripts - missing bgziptabix
After a look at the CMakeLists.txt file, I very much get the impression
that the current vcflib package also misses the BINs, not ony the SCRIPTs.
Best,
Steffen
Am 23.05.21 um 17:02 schrieb Pjotr Prins:
> 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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