Remove bedtools and bowtie

[donald]

Can we remove these two rather unmaintained packages from /usr/bin? These are installed with newer versions in /package/sequencer and available via /usr/local/package/bin.

buczek@theinternet:~/git/bee-files (remove-bedtools-and-bowtie)$ fakeroot bee query bowtie-1.0.0_p8_8087dd6-0.x86_64
/usr/bin/bowtie-inspect
/usr/bin/bowtie-build
/usr/bin/bowtie
buczek@theinternet:~/git/bee-files (remove-bedtools-and-bowtie)$ fakeroot bee query bedtools-2.29.2-0.x86_64
/usr/bin/windowBed
/usr/bin/mapBed
/usr/bin/multiBamCov
/usr/bin/maskFastaFromBed
/usr/bin/mergeBed
/usr/bin/subtractBed
/usr/bin/coverageBed
/usr/bin/windowMaker
/usr/bin/groupBy
/usr/bin/intersectBed
/usr/bin/complementBed
/usr/bin/fastaFromBed
/usr/bin/getOverlap
/usr/bin/multiIntersectBed
/usr/bin/slopBed
/usr/bin/randomBed
/usr/bin/clusterBed
/usr/bin/linksBed
/usr/bin/closestBed
/usr/bin/bamToFastq
/usr/bin/shiftBed
/usr/bin/bedToBam
/usr/bin/genomeCoverageBed
/usr/bin/flankBed
/usr/bin/annotateBed
/usr/bin/bamToBed
/usr/bin/expandCols
/usr/bin/pairToBed
/usr/bin/shuffleBed
/usr/bin/tagBam
/usr/bin/sortBed
/usr/bin/nucBed
/usr/bin/bedtools
/usr/bin/bedpeToBam
/usr/bin/unionBedGraphs
/usr/bin/bed12ToBed6
/usr/bin/bedToIgv
/usr/bin/pairToPair

[donald]

@sklages: Ping

[donald]

Hmmm. OTOH, except the bedtools commands itself, all of the commands shown above for the bedtools packages are NOT available via /package/sequencer. How comes and will the user miss something?

[sklages]

Hmmm. OTOH, except the bedtools commands itself, all of the commands shown above for the bedtools packages are NOT available via /package/sequencer. How comes and will the user miss something?

Yes, my bad. The binary bedtools is usually the only program needed. All other programs of this package are only wrappers calling bedtools with the corresponding sub-command, e.g.:

# bamToBed
cat bamToBed

#!/bin/sh
${0%/*}/bedtools bamtobed "$@"

But I agree with you that we should provide the "complete" bedtools ... some people may rely on these wrappers :-)

I have updated sequencer.include accordingly ..

[donald]

Nice, thanks.

[thomas]

Well, guess it is too late for a 'review' now. But it looks good to me.

[donald]

Never to late :-)