1 files changed, 35 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix b/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix
new file mode 100644
index 000000000000..0ceaab4ab46b
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix
@@ -0,0 +1,35 @@
+{ lib, stdenv, fetchFromGitHub, zlib, bzip2, xz }:
+
+stdenv.mkDerivation rec {
+  pname = "freebayes";
+  version = "1.3.1";
+
+  src = fetchFromGitHub {
+    name = "freebayes-${version}-src";
+    owner  = "ekg";
+    repo   = "freebayes";
+    rev    = "v${version}";
+    sha256 = "035nriknjqq8gvil81vvsmvqwi35v80q8h1cw24vd1gdyn1x7bys";
+    fetchSubmodules = true;
+  };
+
+  buildInputs = [ zlib bzip2 xz ];
+
+  # Workaround build failure on -fno-common toolchains like upstream
+  # gcc-10. Otherwise build fails as:
+  #   ld: foomatic_rip-options.o:/build/foomatic-filters-4.0.17/options.c:49: multiple definition of `cupsfilter';
+  #     foomatic_rip-foomaticrip.o:/build/foomatic-filters-4.0.17/foomaticrip.c:158: first defined here
+  env.NIX_CFLAGS_COMPILE = "-fcommon";
+
+  installPhase = ''
+    install -vD bin/freebayes bin/bamleftalign scripts/* -t $out/bin
+  '';
+
+  meta = with lib; {
+    description = "Bayesian haplotype-based polymorphism discovery and genotyping";
+    license     = licenses.mit;
+    homepage    = "https://github.com/ekg/freebayes";
+    maintainers = with maintainers; [ jdagilliland ];
+    platforms = [ "x86_64-linux" ];
+  };
+}