Re: [PATCH] gnu: Add bedtools

[Mark H Weaver]

Ricardo Wurmus <address@hidden> writes:

> From c8d71da303ff6b82a30db542d382cab57a00699e Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <address@hidden>
> 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