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{stdenv, fetchFromGitHub, nim, htslib, pcre}:
let
hts-nim = fetchFromGitHub {
owner = "brentp";
repo = "hts-nim";
rev = "v0.2.5";
sha256 = "1fma99rjqxgg9dihkd10hm1jjp5amsk5wsxnvq1lk4mcsjix5xqb";
};
docopt = fetchFromGitHub {
owner = "docopt";
repo = "docopt.nim";
rev = "v0.6.5";
sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr";
};
in stdenv.mkDerivation rec {
name = "mosdepth-${version}";
version = "0.2.3";
src = fetchFromGitHub {
owner = "brentp";
repo = "mosdepth";
rev = "v${version}";
sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7";
};
buildInputs = [ nim ];
buildPhase = ''
HOME=$TMPDIR
nim -p:${hts-nim}/src -p:${docopt}/src c --nilseqs:on -d:release mosdepth.nim
'';
installPhase = "install -Dt $out/bin mosdepth";
fixupPhase = "patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ stdenv.cc.cc htslib pcre ]} $out/bin/mosdepth";
meta = with stdenv.lib; {
description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.";
license = licenses.mit;
homepage = https://github.com/brentp/mosdepth;
maintainers = with maintainers; [ jbedo ];
platforms = platforms.linux;
};
}
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