Ihar Hrachyshka
567e8dfd8e
This commit was created by a combination of scripts and tools: - an ast-grep script to prefix things in meta with `lib.`, - a modified nixf-diagnose / nixf combination to remove unused `with lib;`, and - regular nixfmt. Co-authored-by: Wolfgang Walther <walther@technowledgy.de>
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 = {
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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 = lib.licenses.artistic2;
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maintainers = with lib.maintainers; [ apraga ];
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};
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}
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