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htslib: 1.7 -> 1.9 #46270

Merged
merged 1 commit into from Oct 6, 2018
Merged

htslib: 1.7 -> 1.9 #46270

merged 1 commit into from Oct 6, 2018

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r-ryantm
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@r-ryantm r-ryantm commented Sep 7, 2018

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from htslib.

meta.description for htslib is: '"A C library for reading/writing high-throughput sequencing data"'.

Checks done (click to expand)
  • built on NixOS
  • /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/bin/bgzip passed the binary check.
  • /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/bin/htsfile passed the binary check.
  • /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/bin/tabix passed the binary check.
  • 3 of 3 passed binary check by having a zero exit code.
  • 0 of 3 passed binary check by having the new version present in output.
  • found 1.9 with grep in /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9
  • directory tree listing: https://gist.github.com/b5abdcff796e6a95f05e5e2ac62113dd
  • du listing: https://gist.github.com/ae15a6f06377418b0d73639655ac9296
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/cb787e9426ef91bdb95b944db47244657ae96523.tar.gz -p htslib
ls -la /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9

cc @mimadrid for testing.

htslib: 1.7 -> 1.9
cb787e9 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
htslib
@GrahamcOfBorg
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Success on x86_64-darwin (full log)

Attempted: htslib

Partial log (click to expand)

install -p -m 644 htslib/*.h /nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9/include/htslib
install -p -m 644 libhts.a /nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9/lib/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9/share/man/man5
post-installation fixup
gzipping man pages under /nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9/share/man/
strip is /nix/store/df6k4mgdjxciy0f637lryp7c9ln7n1m3-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9/lib  /nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9/bin
patching script interpreter paths in /nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9
/nix/store/hakym2r1shp1hlgj6cav2x2gqv3fmfnj-htslib-1.9

@GrahamcOfBorg
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Success on aarch64-linux (full log)

Attempted: htslib

Partial log (click to expand)

shrinking /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9/lib/libhts.so.1.9
shrinking /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9/bin/tabix
shrinking /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9/bin/htsfile
shrinking /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9/bin/bgzip
gzipping man pages under /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9/share/man/
strip is /nix/store/y4ymnvgxygpq05h03kyzbj572zmh6zla-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9/lib  /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9/bin
patching script interpreter paths in /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9
checking for references to /build in /nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9...
/nix/store/8pf47w5zxdvvf0n0550hdkh6kzj96kkw-htslib-1.9

@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: htslib

Partial log (click to expand)

shrinking /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/lib/libhts.so.1.9
shrinking /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/bin/bgzip
shrinking /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/bin/htsfile
shrinking /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/bin/tabix
gzipping man pages under /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/share/man/
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/lib  /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9/bin
patching script interpreter paths in /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9
checking for references to /build in /nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9...
/nix/store/a80adzckf07wnrhniyakgn9v9isy3zvq-htslib-1.9

@matthewbauer matthewbauer merged commit 54c0a2a into NixOS:master Oct 6, 2018
@r-ryantm r-ryantm deleted the auto-update/htslib branch October 13, 2018 22:21
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