diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix index 13094e7484e6..3e2188a93d10 100644 --- a/pkgs/applications/science/biology/mosdepth/default.nix +++ b/pkgs/applications/science/biology/mosdepth/default.nix @@ -1,4 +1,4 @@ -{lib, nimPackages, fetchFromGitHub, pcre}: +{ lib, nimPackages, fetchFromGitHub, docopt, hts, pcre }: nimPackages.buildNimPackage rec { pname = "mosdepth"; @@ -12,7 +12,7 @@ nimPackages.buildNimPackage rec { sha256 = "sha256-7uteYTCbAaXedPqk0WtHpqTfUWH/+rRW8aSlFixkEko="; }; - buildInputs = with nimPackages; [ docopt hts-nim pcre ]; + buildInputs = [ docopt hts pcre ]; meta = with lib; { description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing"; diff --git a/pkgs/development/nim-packages/hts-nim/default.nix b/pkgs/development/nim-packages/hts-nim/default.nix deleted file mode 100644 index d536133ce9b0..000000000000 --- a/pkgs/development/nim-packages/hts-nim/default.nix +++ /dev/null @@ -1,14 +0,0 @@ -{ buildNimPackage, fetchFromGitHub, htslib }: - -buildNimPackage rec { - pname = "hts-nim"; - version = "0.3.4"; - src = fetchFromGitHub { - owner = "brentp"; - repo = pname; - rev = "v${version}"; - sha256 = "0670phk1bq3l9j2zaa8i5wcpc5dyfrc0l2a6c21g0l2mmdczffa7"; - }; - propagatedBuildInputs = [ htslib ]; - doCheck = false; -} diff --git a/pkgs/development/nim-packages/hts/default.nix b/pkgs/development/nim-packages/hts/default.nix new file mode 100644 index 000000000000..1cf763d77b16 --- /dev/null +++ b/pkgs/development/nim-packages/hts/default.nix @@ -0,0 +1,21 @@ +{ lib, buildNimPackage, fetchFromGitHub, htslib }: + +buildNimPackage (final: prev: { + pname = "hts"; + version = "0.3.23"; + src = fetchFromGitHub { + owner = "brentp"; + repo = "hts-nim"; + rev = "v${final.version}"; + hash = "sha256-o27yOtzW4hk8dpicqjW4D8zxqXHdxcz+e84PyK+yBq8="; + }; + propagatedBuildInputs = [ htslib ]; + nimFlags = [ "--mm:refc" ]; + doCheck = false; + meta = final.src.meta // { + description = "Nim wrapper for htslib for parsing genomics data files"; + homepage = "https://brentp.github.io/hts-nim/"; + license = [ lib.licenses.mit ]; + maintainers = with lib.maintainers; [ ehmry ]; + }; +}) diff --git a/pkgs/top-level/nim-packages.nix b/pkgs/top-level/nim-packages.nix index 5c379034176a..628da7adca6f 100644 --- a/pkgs/top-level/nim-packages.nix +++ b/pkgs/top-level/nim-packages.nix @@ -46,7 +46,7 @@ lib.makeScope newScope (self: hashlib = callPackage ../development/nim-packages/hashlib { }; - hts-nim = callPackage ../development/nim-packages/hts-nim { }; + hts = callPackage ../development/nim-packages/hts { }; illwill = callPackage ../development/nim-packages/illwill { };