From 323c503cbabc14dd12e040306c974c0c42a826f5 Mon Sep 17 00:00:00 2001
From: Emery Hemingway <ehmry@posteo.net>
Date: Thu, 2 Sep 2021 18:35:32 +0200
Subject: [PATCH] mosdepth: convert to buildNimPackage

---
 .../science/biology/mosdepth/default.nix      | 30 +++----------------
 .../nim-packages/docopt/default.nix           |  8 +++++
 .../nim-packages/hts-nim/default.nix          | 13 ++++++++
 pkgs/top-level/nim-packages.nix               |  4 +++
 4 files changed, 29 insertions(+), 26 deletions(-)
 create mode 100644 pkgs/development/nim-packages/docopt/default.nix
 create mode 100644 pkgs/development/nim-packages/hts-nim/default.nix

diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix
index 715f2ea313b..b6cc5e40615 100644
--- a/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/pkgs/applications/science/biology/mosdepth/default.nix
@@ -1,23 +1,9 @@
-{lib, stdenv, fetchFromGitHub, nim, htslib, pcre}:
+{lib, nimPackages, fetchFromGitHub, pcre}:
 
-let
-  hts-nim = fetchFromGitHub {
-    owner = "brentp";
-    repo = "hts-nim";
-    rev = "v0.3.4";
-    sha256 = "0670phk1bq3l9j2zaa8i5wcpc5dyfrc0l2a6c21g0l2mmdczffa7";
-  };
-
-  docopt = fetchFromGitHub {
-    owner = "docopt";
-    repo = "docopt.nim";
-    rev = "v0.6.7";
-    sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37";
-  };
-
-in stdenv.mkDerivation rec {
+nimPackages.buildNimPackage rec {
   pname = "mosdepth";
   version = "0.3.2";
+  nimBinOnly = true;
 
   src = fetchFromGitHub {
     owner = "brentp";
@@ -26,15 +12,7 @@ in stdenv.mkDerivation rec {
     sha256 = "sha256-uui4yC7ok+pvbXVKfBVsAarH40fnH4fnP8P4uzOqztQ=";
   };
 
-  nativeBuildInputs = [ nim ];
-  buildInputs = [ htslib pcre ];
-
-  buildPhase = ''
-    HOME=$TMPDIR
-    nim -p:${hts-nim}/src -p:${docopt}/src c --nilseqs:on -d:release mosdepth.nim
-  '';
-
-  installPhase = "install -Dt $out/bin mosdepth";
+  buildInputs = with nimPackages; [ docopt hts-nim pcre ];
 
   meta = with lib; {
     description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing";
diff --git a/pkgs/development/nim-packages/docopt/default.nix b/pkgs/development/nim-packages/docopt/default.nix
new file mode 100644
index 00000000000..38465384fbd
--- /dev/null
+++ b/pkgs/development/nim-packages/docopt/default.nix
@@ -0,0 +1,8 @@
+{ fetchFromGitHub }:
+
+fetchFromGitHub {
+  owner = "docopt";
+  repo = "docopt.nim";
+  rev = "v0.6.7";
+  sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37";
+}
diff --git a/pkgs/development/nim-packages/hts-nim/default.nix b/pkgs/development/nim-packages/hts-nim/default.nix
new file mode 100644
index 00000000000..960a9e63d21
--- /dev/null
+++ b/pkgs/development/nim-packages/hts-nim/default.nix
@@ -0,0 +1,13 @@
+{ 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 ];
+}
diff --git a/pkgs/top-level/nim-packages.nix b/pkgs/top-level/nim-packages.nix
index a1cefc4fd81..7d9e6c512f4 100644
--- a/pkgs/top-level/nim-packages.nix
+++ b/pkgs/top-level/nim-packages.nix
@@ -16,10 +16,14 @@ lib.makeScope newScope (self:
 
     chroma = callPackage ../development/nim-packages/chroma { };
 
+    docopt = callPackage ../development/nim-packages/docopt { };
+
     flatty = callPackage ../development/nim-packages/flatty { };
 
     frosty = callPackage ../development/nim-packages/frosty { };
 
+    hts-nim = callPackage ../development/nim-packages/hts-nim { };
+
     jester = callPackage ../development/nim-packages/jester { };
 
     jsonschema = callPackage ../development/nim-packages/jsonschema { };