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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/picard-tools/versions
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Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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hisat2: init 2.1.0
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Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
picard-tools
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bowtie2: 2.3.4.1 -> 2.3.4.2
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never built as far back as hydra logs go.
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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/bowtie2/versions.
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strelka: init 2.9.5
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Hydra: ?compare=1473892
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Conflicts: gobby and libinfinity - I took the hand-edited versions
instead of those resuting from the mass-replacement.
Hydra: ?compare=1473190
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igv: 2.4.13 -> 2.4.14
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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/igv/versions.
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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/picard-tools/versions.
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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/vcftools/versions.
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to fix non-deterministic failure
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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/bcftools/versions.
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picard-tools: 2.18.9 -> 2.18.10
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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/picard-tools/versions.
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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/igv/versions.
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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/igv/versions.
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11/bin/igv had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.4.11 with grep in /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11
- directory tree listing: https://gist.github.com/ca4cf484aab1c1590806c47c4fdde1d7
- du listing: https://gist.github.com/f7ff80a2429cf0a942195db4944659b1
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mosdepth: init 0.2.3
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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/picard-tools/versions.
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.9 with grep in /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9
- directory tree listing: https://gist.github.com/0972acdc51fe8a1cde470e4ab5e87993
- du listing: https://gist.github.com/6a66b6723ce4887cd108678369b87360
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hmmer: init at 3.1b2
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* treewide: http -> https sources
This updates the source urls of all top-level packages from http to
https where possible.
* buildtorrent: fix url and tab -> spaces
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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/picard-tools/versions.
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.7 with grep in /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7
- directory tree listing: https://gist.github.com/a49ed5f2ff312ce6180174183901e38f
- du listing: https://gist.github.com/243f4d89d2100ef27d332e3562d5f173
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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/RAxML/versions.
These checks were done:
- built on NixOS
- /nix/store/w8iy7fvdwhjw7zx1dkga3v56fz59s7r8-RAxML-8.2.12/bin/raxmlHPC-PTHREADS-SSE3 passed the binary check.
- 1 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 8.2.12 with grep in /nix/store/w8iy7fvdwhjw7zx1dkga3v56fz59s7r8-RAxML-8.2.12
- directory tree listing: https://gist.github.com/8a2b70b299e53bfee9f18d2ab8cd5f9f
- du listing: https://gist.github.com/02803409663f19671adc6be233a327fd
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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/picard-tools/versions.
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.5 with grep in /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5
- directory tree listing: https://gist.github.com/1938ad634fa882d94e8d28fd1625547c
- du listing: https://gist.github.com/4b51e89646327900f6ef6f2242f5d0bd
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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/picard-tools/versions.
These checks were done:
- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.4 with grep in /nix/store/k62ym9i08d0w9sgmdjjfyy4lf2n9ig7p-picard-tools-2.18.4
- directory tree listing: https://gist.github.com/4d9e3062e701681d9b53033dc9511663
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picard-tools: 2.18.2 -> 2.18.3
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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/picard-tools/versions.
These checks were done:
- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.3 with grep in /nix/store/q67hqz7716nf3c4f8rjmlpf2dqbb06rz-picard-tools-2.18.3
- directory tree listing: https://gist.github.com/6b71ce718f18ef6a48c05457cd0e583b
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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/paml/versions.
These checks were done:
- built on NixOS
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 -h’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 --help’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 help’ got 0 exit code
- found 4.9h with grep in /nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h
- directory tree listing: https://gist.github.com/b2a37e7cd2b4b41178f0698f3aac69e2
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picard-tools: 2.18.1 -> 2.18.2
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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/picard-tools/versions.
These checks were done:
- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.2 with grep in /nix/store/sp6gc6c6knpvpsmfdx8074qclcsgs931-picard-tools-2.18.2
- directory tree listing: https://gist.github.com/114857d15222eccda94501b5a871fb24
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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
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