From: Mark H Weaver <mhw@netris.org>
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: guix-devel@gnu.org
Subject: Re: [PATCH] gnu: Add bedtools
Date: Sat, 13 Dec 2014 01:42:59 -0500 [thread overview]
Message-ID: <87fvckyrrg.fsf@netris.org> (raw)
In-Reply-To: <idj388lkwih.fsf@bimsb-sys02.mdc-berlin.net> (Ricardo Wurmus's message of "Fri, 12 Dec 2014 11:11:50 +0100")
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
> From c8d71da303ff6b82a30db542d382cab57a00699e Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 11 Dec 2014 17:37:16 +0100
> Subject: [PATCH] gnu: Add bedtools
Ludovic mostly covered this, but I have two additional suggestions:
> + (alist-replace
> + 'install (lambda* (#:key outputs #:allow-other-keys)
Please align the lambda* under 'install.
> + (let* ((out (assoc-ref outputs "out"))
> + (bin (string-append out "/bin"))
> + (tools
> + '("bamToFastq" "mapBed" "shuffleBed" "bed12ToBed6" "bedToBam"
> + "multiIntersectBed" "complementBed" "randomBed" "tagBam" "sortBed"
> + "annotateBed" "clusterBed" "fastaFromBed" "coverageBed" "bedpeToBam"
> + "pairToPair" "subtractBed" "nucBed" "expandCols" "bedToIgv" "slopBed"
> + "closestBed" "windowMaker" "linksBed" "getOverlap" "mergeBed" "windowBed"
> + "flankBed" "pairToBed" "intersectBed" "bamToBed" "multiBamCov"
> + "unionBedGraphs" "genomeCoverageBed" "groupBy" "maskFastaFromBed"
> + "bedtools")))
> + (mkdir-p bin)
> + (map (lambda (tool)
It would be more appropriate to use 'for-each' here instead of 'map'.
> + (copy-file (string-append "bin/" tool)
> + (string-append bin "/" tool)))
> + tools)))
> + %standard-phases)))))
[...]
Thanks!
Mark
next prev parent reply other threads:[~2014-12-13 6:42 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-12-12 10:11 [PATCH] gnu: Add bedtools Ricardo Wurmus
2014-12-12 23:00 ` Ludovic Courtès
2014-12-13 6:42 ` Mark H Weaver [this message]
2014-12-15 15:46 ` Ricardo Wurmus
2014-12-16 17:18 ` Ludovic Courtès
[not found] <20141215155541.GA19757@jocasta.intra>
[not found] ` <idj61db7vu0.fsf@bimsb-sys02.mdc-berlin.net>
2014-12-16 10:15 ` John Darrington
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