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{
BioPerl,
IOString,
buildPerlModule,
fetchFromGitHub,
fetchpatch,
fetchurl,
kent,
lib,
libmysqlclient,
libpng,
openssl,
perl
}:
buildPerlModule rec {
pname = "Bio-BigFile";
version = "1.07";
src = fetchurl {
url = "mirror://cpan/authors/id/L/LD/LDS/Bio-BigFile-${version}.tar.gz";
sha256 = "277b66ce8acbdd52399e2c5a0cf4e3bd5c74c12b94877cd383d0c4c97740d16d";
};
# Only kent 335 works with Bio-BigFile, see
# - official documentation: https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#bigfile
# - one of the developer's answer: https://github.com/Ensembl/ensembl-vep/issues/1412
# BioBigfile needs the environment variable KENT_SRC to find kent
KENT_SRC = kent.overrideAttrs (old: rec {
pname = "kent";
version = "335";
src = fetchFromGitHub {
owner = "ucscGenomeBrowser";
repo = "kent";
rev = "v${version}_base";
sha256 = "1455dwzpaq4hyhcqj3fpwgq5a39kp46qarfbr6ms6l2lz583r083";
};
patches = [
# Fix for linking error with zlib. Adding zlib as a dependency is not enough
./kent-utils.patch
# Vendoring upstream patch (not merged in uscsGenomeBrowser/kent)
./kent-316e4fd40f53c96850128fd65097a42623d1e736.patch
];
});
buildInputs = [
BioPerl
IOString
libpng
libmysqlclient
openssl
];
# Ensure compatibility with GCC-11 (compilation fails if -Wno-format-security)
hardeningDisable = [ "format" ];
meta = with lib; {
homepage = "https://metacpan.org/dist/Bio-BigFile";
description = "Manipulate Jim Kent's BigWig and BigBed index files for genomic features";
license = licenses.artistic2;
maintainers = with maintainers; [ apraga ];
};
}
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