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][email protected]> >>> 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:[email protected]
