mosdepth: build with a lockfile

pkgs/by-name/mo/mosdepth/lock.json

@@ -0,0 +1,64 @@
+{
+  "depends": [
+    {
+      "method": "fetchzip",
+      "packages": [
+        "d4"
+      ],
+      "path": "/nix/store/gc6hspl4p050mrlm3v3gj6pw87rp3awj-source",
+      "ref": "v0.0.3",
+      "rev": "3536104b4070ff617537ef37db7cfbae36909546",
+      "sha256": "12n5snrxha27hz95qq7krgrmip39xvhb400y5b0awnh44gczwn90",
+      "srcDir": "src",
+      "url": "https://github.com/brentp/d4-nim/archive/3536104b4070ff617537ef37db7cfbae36909546.tar.gz"
+    },
+    {
+      "method": "fetchzip",
+      "packages": [
+        "docopt"
+      ],
+      "path": "/nix/store/qdmip0p56pd5ivalp3waaqjkc1xvzaxn-source",
+      "ref": "v0.7.1",
+      "rev": "efaa112b6df172a9168c4eb581ab8dda1fbcfe2a",
+      "sha256": "0v85frvfm5difggs016g8llspsq8kd27lq00sv79v65ih9vlr9r4",
+      "srcDir": "src",
+      "url": "https://github.com/docopt/docopt.nim/archive/efaa112b6df172a9168c4eb581ab8dda1fbcfe2a.tar.gz"
+    },
+    {
+      "method": "fetchzip",
+      "packages": [
+        "hts"
+      ],
+      "path": "/nix/store/k19hyryn922gy9f9xmdrj6i80p1npgk0-source",
+      "ref": "v0.3.25",
+      "rev": "e70f16a008d1c6526fa8c108c73968175505d9d0",
+      "sha256": "1pcvqp9lnsl575f13hf6rxg2pb0lsq6z1wi4pzva5yjv5cmwq3pk",
+      "srcDir": "src",
+      "url": "https://github.com/brentp/hts-nim/archive/e70f16a008d1c6526fa8c108c73968175505d9d0.tar.gz"
+    },
+    {
+      "method": "fetchzip",
+      "packages": [
+        "regex"
+      ],
+      "path": "/nix/store/vfs4ysdw2kvyp18jwpbvb9wfh1ajz0a9-source",
+      "ref": "v0.23.0",
+      "rev": "577c4ec3b235c5fd2653a9c86cbc4a576cfc0869",
+      "sha256": "0401f9m2m2h6bikl3hffyhaw5fc2nbjdf5mj4z9wckmm9lx9hpkl",
+      "srcDir": "src",
+      "url": "https://github.com/nitely/nim-regex/archive/577c4ec3b235c5fd2653a9c86cbc4a576cfc0869.tar.gz"
+    },
+    {
+      "method": "fetchzip",
+      "packages": [
+        "unicodedb"
+      ],
+      "path": "/nix/store/wpilzdf8vdwp7w129yrl821p9qvl3ky3-source",
+      "ref": "0.12.0",
+      "rev": "b055310c08db8f879057b4fec15c8301ee93bb2a",
+      "sha256": "0w77h75vrgp6jiq4dd9i2m4za2cf8qhjkz2wlxiz27yn2isjrndy",
+      "srcDir": "src",
+      "url": "https://github.com/nitely/nim-unicodedb/archive/b055310c08db8f879057b4fec15c8301ee93bb2a.tar.gz"
+    }
+  ]
+}

pkgs/by-name/mo/mosdepth/package.nix

@@ -1,19 +1,27 @@
-{ lib, nimPackages, fetchFromGitHub, docopt, hts, pcre }:
+{ lib, buildNimPackage, fetchFromGitHub, pcre, testers }:
 
-nimPackages.buildNimPackage rec {
+buildNimPackage (finalAttrs: {
   pname = "mosdepth";
   version = "0.3.5";
-  nimBinOnly = true;
+
+  requiredNimVersion = 1;
 
   src = fetchFromGitHub {
     owner = "brentp";
     repo = "mosdepth";
-    rev = "v${version}";
+    rev = "v${finalAttrs.version}";
     sha256 = "sha256-tG3J51PS6A0WBCZ+j/Nf7aaukFV+DZJsxpbTbvwu0zc=";
   };
 
-  buildInputs = [ docopt hts pcre ];
-  nimFlags = hts.nimFlags ++ [ "--threads:off" ];
+  lockFile = ./lock.json;
+
+  buildInputs = [ pcre ];
+
+  passthru.tests = {
+    version = testers.testVersion {
+      package = finalAttrs.finalPackage;
+    };
+  };
 
   meta = with lib; {
     description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing";
@@ -22,4 +30,4 @@ nimPackages.buildNimPackage rec {
     maintainers = with maintainers; [ jbedo ];
     platforms = platforms.linux;
   };
-}
+})

pkgs/top-level/all-packages.nix

@@ -39078,8 +39078,6 @@ with pkgs;
     inherit (llvmPackages) openmp;
   };
 
-  mosdepth = nim2Packages.callPackage ../applications/science/biology/mosdepth { };
-
   niftyreg = callPackage ../applications/science/biology/niftyreg { };
 
   niftyseg = callPackage ../applications/science/biology/niftyseg { };

pkgs/top-level/nim-overrides.nix

@@ -1,5 +1,6 @@
 { lib
 , stdenv
+, htslib
 , libsass
 , openssl
 , SDL2
@@ -15,6 +16,11 @@
       buildInputs = buildInputs ++ [ openssl ];
     };
 
+  hts = lockAttrs: finalAttrs:
+    { buildInputs ? [ ], ... }: {
+      buildInputs = buildInputs ++ [ htslib ];
+    };
+
   sass = lockAttrs: finalAttrs:
     { buildInputs ? [ ], ... }: {
       buildInputs = buildInputs ++ [ libsass ];