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samtools-old: init at 0.1.19 #34530

Merged
merged 1 commit into from Feb 10, 2018
Merged

samtools-old: init at 0.1.19 #34530

merged 1 commit into from Feb 10, 2018

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unode
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@unode unode commented Feb 2, 2018

Motivation for this change

nixpkgs already contains samtools-1.5 but some software still requires the older 0.1.19 version.

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.

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unode commented Feb 2, 2018

@mimadrid as maintainer of the more recent samtools version, feedback is appreciated. Cheers.

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unode commented Feb 2, 2018

@GrahamcOfBorg build samtools-old

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Success on x86_64-linux (full log)

Partial log (click to expand)

installing
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/x0kpj4bc4fxawkl7mfamgp0lkx2dd3bp-samtools-0.1.19
shrinking /nix/store/x0kpj4bc4fxawkl7mfamgp0lkx2dd3bp-samtools-0.1.19/bin/samtools
gzipping man pages under /nix/store/x0kpj4bc4fxawkl7mfamgp0lkx2dd3bp-samtools-0.1.19/share/man/
strip is /nix/store/mdyy001q67hiks0g24ra53z7ckm4jfr4-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/x0kpj4bc4fxawkl7mfamgp0lkx2dd3bp-samtools-0.1.19/bin 
patching script interpreter paths in /nix/store/x0kpj4bc4fxawkl7mfamgp0lkx2dd3bp-samtools-0.1.19
checking for references to /tmp/nix-build-samtools-0.1.19.drv-0 in /nix/store/x0kpj4bc4fxawkl7mfamgp0lkx2dd3bp-samtools-0.1.19...
/nix/store/x0kpj4bc4fxawkl7mfamgp0lkx2dd3bp-samtools-0.1.19

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Success on aarch64-linux (full log)

Partial log (click to expand)

installing
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/vh1va0nkzp5jgkrrgzy9vlrjkisz6pbx-samtools-0.1.19
shrinking /nix/store/vh1va0nkzp5jgkrrgzy9vlrjkisz6pbx-samtools-0.1.19/bin/samtools
gzipping man pages under /nix/store/vh1va0nkzp5jgkrrgzy9vlrjkisz6pbx-samtools-0.1.19/share/man/
strip is /nix/store/jwz859pxqj7sl2dbwvmxkx68jp774izb-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/vh1va0nkzp5jgkrrgzy9vlrjkisz6pbx-samtools-0.1.19/bin
patching script interpreter paths in /nix/store/vh1va0nkzp5jgkrrgzy9vlrjkisz6pbx-samtools-0.1.19
checking for references to /build in /nix/store/vh1va0nkzp5jgkrrgzy9vlrjkisz6pbx-samtools-0.1.19...
/nix/store/vh1va0nkzp5jgkrrgzy9vlrjkisz6pbx-samtools-0.1.19

dotlambda
dotlambda reviewed Feb 2, 2018
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@dotlambda dotlambda left a comment •
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Why do you need a new derivation? Isn't it possible to override samtools and add samtools-old = samtools.overrideAttrs ...?

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unode commented Feb 2, 2018

I don't know enough about nix yet to follow your suggestion. However, from what I gathered I'd have to override almost every attribute in the existing samtools derivation.
Diferent url and homepage, different dependencies, checks, and installation. The only thing in common is the description, license and zlib dependency.

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dotlambda commented Feb 2, 2018 •
edited

Then it doesn't make much sense, you're right.
You might however want to rename the attribute to samtools_0_1_19 as this is more common in Nixpkgs and put the derivation in the same folder as samtools.

To learn more about overrideAttrs, look here.

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samtools_0_1_19: init at 0.1.19
65ea5f8 
samtools-1.5 already exists but some software requires the older version
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mimame commented Feb 6, 2018

@unode Awesome, thanks a lot. I think it's ok now to be merged

@Mic92 Mic92 merged commit 08d1400 into NixOS:master Feb 10, 2018
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@unode @GrahamcOfBorg @dotlambda @mimame @Mic92