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bedtools: 2.26.0 -> 2.27.1 #34139

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merged 1 commit into from Jan 23, 2018
Merged

bedtools: 2.26.0 -> 2.27.1 #34139

merged 1 commit into from Jan 23, 2018

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arcadio
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@arcadio arcadio commented Jan 22, 2018

Motivation for this change

Upgrade bedtools to latest stable release.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Fits CONTRIBUTING.md.

@jbedo

@Mic92
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Mic92 commented Jan 22, 2018

@GrahamcOfBorg build bedtools

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Success for system: x86_64-darwin

/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/shiftBed: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/shuffleBed: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/slopBed: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/sortBed: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/subtractBed: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/tagBam: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/unionBedGraphs: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/windowBed: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1/bin/windowMaker: interpreter directive changed from "/bin/sh" to "/nix/store/4cvvpbqdkrb0hr4p47q3s9l2a6k04y1g-bash-4.4-p12/bin/sh"
/nix/store/3k522k29b0sipplvh9cjx23rf37pq13i-bedtools-2.27.1

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Success for system: x86_64-linux

/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1/bin/randomBed: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1/bin/fastaFromBed: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1/bin/mapBed: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1/bin/flankBed: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1/bin/maskFastaFromBed: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1/bin/complementBed: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1/bin/tagBam: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1/bin/expandCols: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
checking for references to /tmp/nix-build-bedtools-2.27.1.drv-0 in /nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1...
/nix/store/kd71gxcqwgna20bxshzw8jmii0pfdkmg-bedtools-2.27.1

@adisbladis adisbladis merged commit b0603f5 into NixOS:master Jan 23, 2018
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Success for system: aarch64-linux

/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1/bin/closestBed: interpreter directive changed from "/bin/sh" to "/nix/store/rc78viijga8i0m4imrnqk8d1csyqr8yx-bash-4.4-p12/bin/sh"
/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1/bin/bedpeToBam: interpreter directive changed from "/bin/sh" to "/nix/store/rc78viijga8i0m4imrnqk8d1csyqr8yx-bash-4.4-p12/bin/sh"
/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1/bin/bedToIgv: interpreter directive changed from "/bin/sh" to "/nix/store/rc78viijga8i0m4imrnqk8d1csyqr8yx-bash-4.4-p12/bin/sh"
/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1/bin/bedToBam: interpreter directive changed from "/bin/sh" to "/nix/store/rc78viijga8i0m4imrnqk8d1csyqr8yx-bash-4.4-p12/bin/sh"
/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1/bin/bed12ToBed6: interpreter directive changed from "/bin/sh" to "/nix/store/rc78viijga8i0m4imrnqk8d1csyqr8yx-bash-4.4-p12/bin/sh"
/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1/bin/bamToFastq: interpreter directive changed from "/bin/sh" to "/nix/store/rc78viijga8i0m4imrnqk8d1csyqr8yx-bash-4.4-p12/bin/sh"
/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1/bin/bamToBed: interpreter directive changed from "/bin/sh" to "/nix/store/rc78viijga8i0m4imrnqk8d1csyqr8yx-bash-4.4-p12/bin/sh"
/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1/bin/annotateBed: interpreter directive changed from "/bin/sh" to "/nix/store/rc78viijga8i0m4imrnqk8d1csyqr8yx-bash-4.4-p12/bin/sh"
checking for references to /build in /nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1...
/nix/store/jd0ckfy0723mjn7j88xlwsbbi562np34-bedtools-2.27.1

@arcadio arcadio deleted the bedtools branch May 14, 2018 19:21
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4 participants