Silvan Mosberger
4f0dadbf38
After final improvements to the official formatter implementation,
this commit now performs the first treewide reformat of Nix files using it.
This is part of the implementation of RFC 166.
Only "inactive" files are reformatted, meaning only files that
aren't being touched by any PR with activity in the past 2 months.
This is to avoid conflicts for PRs that might soon be merged.
Later we can do a full treewide reformat to get the rest,
which should not cause as many conflicts.
A CI check has already been running for some time to ensure that new and
already-formatted files are formatted, so the files being reformatted here
should also stay formatted.
This commit was automatically created and can be verified using
nix-build https://github.com/infinisil/treewide-nixpkgs-reformat-script/archive/a08b3a4d199c6124ac5b36a889d9099b4383463f.tar.gz \
--argstr baseRev b32a094368
result/bin/apply-formatting $NIXPKGS_PATH
64 lines
1.7 KiB
Nix
64 lines
1.7 KiB
Nix
{
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BioPerl,
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IOString,
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buildPerlModule,
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fetchFromGitHub,
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fetchurl,
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kent,
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lib,
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libmysqlclient,
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libpng,
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openssl,
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}:
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buildPerlModule rec {
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pname = "Bio-BigFile";
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version = "1.07";
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src = fetchurl {
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url = "mirror://cpan/authors/id/L/LD/LDS/Bio-BigFile-${version}.tar.gz";
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sha256 = "277b66ce8acbdd52399e2c5a0cf4e3bd5c74c12b94877cd383d0c4c97740d16d";
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};
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# Only kent 335 works with Bio-BigFile, see
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# - official documentation: https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#bigfile
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# - one of the developer's answer: https://github.com/Ensembl/ensembl-vep/issues/1412
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# BioBigfile needs the environment variable KENT_SRC to find kent
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KENT_SRC = kent.overrideAttrs (old: rec {
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pname = "kent";
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version = "335";
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src = fetchFromGitHub {
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owner = "ucscGenomeBrowser";
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repo = "kent";
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rev = "v${version}_base";
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sha256 = "1455dwzpaq4hyhcqj3fpwgq5a39kp46qarfbr6ms6l2lz583r083";
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};
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patches = [
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# Fix for linking error with zlib. Adding zlib as a dependency is not enough
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./kent-utils.patch
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# Vendoring upstream patch (not merged in uscsGenomeBrowser/kent)
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./kent-316e4fd40f53c96850128fd65097a42623d1e736.patch
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];
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});
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buildInputs = [
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BioPerl
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IOString
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libpng
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libmysqlclient
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openssl
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];
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# Ensure compatibility with GCC-11 (compilation fails if -Wno-format-security)
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hardeningDisable = [ "format" ];
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meta = with lib; {
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homepage = "https://metacpan.org/dist/Bio-BigFile";
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description = "Manipulate Jim Kent's BigWig and BigBed index files for genomic features";
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license = licenses.artistic2;
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maintainers = with maintainers; [ apraga ];
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};
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}
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