Re: vcflib does not install scripts - missing bgziptabix
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
Reply to: