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samtools: 1.7 -> 1.8 #38701

Merged
merged 1 commit into from Apr 17, 2018
Merged

samtools: 1.7 -> 1.8 #38701

merged 1 commit into from Apr 17, 2018

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r-ryantm
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Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/samtools/versions.

These checks were done:

  • built on NixOS
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools --help’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools help’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl -h’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl --help’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl help’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/novo2sam.pl help’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl -h’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl --help’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl help’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl -h’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl --help’ got 0 exit code
  • ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl help’ got 0 exit code
  • found 1.8 with grep in /nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8
  • directory tree listing: https://gist.github.com/4673ea3645eb509035dcb386c4ad1da2

cc @mimadrid for review

samtools: 1.7 -> 1.8
c478b62 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/samtools/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/novo2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl help’ got 0 exit code
- found 1.8 with grep in /nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8
- directory tree listing: https://gist.github.com/4673ea3645eb509035dcb386c4ad1da2
@GrahamcOfBorg
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Success on x86_64-darwin (full log)

Attempted: samtools

Partial log (click to expand)

/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/blast2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/zoom2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/plot-bamstats: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/wgsim_eval.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/soap2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/sam2vcf.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/bowtie2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/novo2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8/bin/psl2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/5spv9lcjwyliipv0yqiv5g8vz0g93v8s-perl-5.24.3/bin/perl"
/nix/store/rnpdc15cny8svb9daadbsi6z4v798xmy-samtools-1.8

@GrahamcOfBorg
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Success on aarch64-linux (full log)

Attempted: samtools

Partial log (click to expand)

/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8/bin/sam2vcf.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/icf1qhlpnbq1gag3x0dp2qsa0kkfvgan-perl-5.24.3/bin/perl"
/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8/bin/psl2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/icf1qhlpnbq1gag3x0dp2qsa0kkfvgan-perl-5.24.3/bin/perl"
/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8/bin/plot-bamstats: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/icf1qhlpnbq1gag3x0dp2qsa0kkfvgan-perl-5.24.3/bin/perl"
/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8/bin/novo2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/icf1qhlpnbq1gag3x0dp2qsa0kkfvgan-perl-5.24.3/bin/perl"
/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8/bin/interpolate_sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/icf1qhlpnbq1gag3x0dp2qsa0kkfvgan-perl-5.24.3/bin/perl"
/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8/bin/export2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/icf1qhlpnbq1gag3x0dp2qsa0kkfvgan-perl-5.24.3/bin/perl"
/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8/bin/bowtie2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/icf1qhlpnbq1gag3x0dp2qsa0kkfvgan-perl-5.24.3/bin/perl"
/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8/bin/blast2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/icf1qhlpnbq1gag3x0dp2qsa0kkfvgan-perl-5.24.3/bin/perl"
checking for references to /build in /nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8...
/nix/store/zv2ixlz59xm9l6w10656a83qnkvprrdw-samtools-1.8

@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: samtools

Partial log (click to expand)

/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/plot-bamstats: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/sam2vcf.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/seq_cache_populate.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/wgsim_eval.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/zoom2sam.pl: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
checking for references to /build in /nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8...
/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8

@matthewbauer matthewbauer merged commit 88098d5 into NixOS:master Apr 17, 2018
@r-ryantm r-ryantm deleted the auto-update/samtools branch April 17, 2018 19:57
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