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bowtie2: 2.3.4.2 -> 2.3.4.3 #47845

Merged
merged 1 commit into from Oct 4, 2018
Merged

bowtie2: 2.3.4.2 -> 2.3.4.3 #47845

merged 1 commit into from Oct 4, 2018

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r-ryantm
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@r-ryantm r-ryantm commented Oct 4, 2018

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/bowtie2/versions.

meta.description for bowtie2 is: '"An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"'.

Release on GitHub

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Checks done (click to expand)
  • built on NixOS
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-inspect passed the binary check.
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-build passed the binary check.
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2 passed the binary check.
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-build-s passed the binary check.
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-build-l passed the binary check.
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-align-s passed the binary check.
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-align-l passed the binary check.
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-inspect-s passed the binary check.
  • /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-inspect-l passed the binary check.
  • 9 of 9 passed binary check by having a zero exit code.
  • 0 of 9 passed binary check by having the new version present in output.
  • found 2.3.4.3 with grep in /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3
  • directory tree listing: https://gist.github.com/3e8f38ccc83cdfec0153cf216c31b020
  • du listing: https://gist.github.com/4f9b81532aecc5ac1a635c66fdd46b4b
Instructions to test this update (click to expand)

One-time optional setup to skip building using Cachix:

  1. Install cachix from https://cachix.org/
  2. Use r-ryantm's cache: 
    cachix use r-ryantm

Test this update by entering a nix shell, seeing what is inside the
result, and if applicable, running some binaries:

nix-shell --pure -I nixpkgs=https://github.com/r-ryantm/nixpkgs/archive/269efba0aa269b5e6dfdd59da64c11b4b360ed5b.tar.gz -p bowtie2
ls -la /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3

cc @rybern for testing.

@r-ryantm
bowtie2: 2.3.4.2 -> 2.3.4.3
269efba 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions
@GrahamcOfBorg
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No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: bowtie2

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowBroken = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowBroken = true; }
to ~/.config/nixpkgs/config.nix.

@GrahamcOfBorg
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Success on x86_64-darwin (full log)

Attempted: bowtie2

Partial log (click to expand)

/nix/store/f2lp21azk4w88f17zgf4mji64agb18ga-bash-4.4-p23/bin/bash: which: command not found
mkdir -p /nix/store/zxc100q46z3p334lriq3kp2bi51q12lv-bowtie2-2.3.4.3/bin
for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \
        cp -f $file /nix/store/zxc100q46z3p334lriq3kp2bi51q12lv-bowtie2-2.3.4.3/bin ; \
done
post-installation fixup
strip is /nix/store/9xjkb4xz0b5lmizij9ppxy7lkxdxhx6b-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/zxc100q46z3p334lriq3kp2bi51q12lv-bowtie2-2.3.4.3/bin
patching script interpreter paths in /nix/store/zxc100q46z3p334lriq3kp2bi51q12lv-bowtie2-2.3.4.3
/nix/store/zxc100q46z3p334lriq3kp2bi51q12lv-bowtie2-2.3.4.3

@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: bowtie2

Partial log (click to expand)

shrinking /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-build-l
shrinking /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-align-l
shrinking /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-align-s
shrinking /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-build-s
shrinking /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin/bowtie2-inspect-s
strip is /nix/store/dxf1m7dhc4qb655bdljc1fsd74v1nag3-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3/bin
patching script interpreter paths in /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3
checking for references to /build in /nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3...
/nix/store/g49idf9v837nmdh1v0m7hqrl48hgx089-bowtie2-2.3.4.3

@Mic92 Mic92 merged commit a24cf5c into NixOS:master Oct 4, 2018
@r-ryantm r-ryantm deleted the auto-update/bowtie2 branch October 13, 2018 22:19
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