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authormarkuskowa <markus.kowalewski@gmail.com>2019-06-27 12:43:25 +0200
committerGitHub <noreply@github.com>2019-06-27 12:43:25 +0200
commita07d045b00a7cf962eca464f648c33ee409a92cf (patch)
tree02cd6848f31eadea3f0f2f8741acdff68484cfe9
parentfdf2700c32998f2d8f21d452f9044a697ff05032 (diff)
parentb8b71aaaf97a63a1b6bf286402faf234affe6bf7 (diff)
Merge pull request #63488 from jbedo/octopus
octopus: init 0.6.3-beta
-rw-r--r--pkgs/applications/science/biology/octopus/default.nix30
-rw-r--r--pkgs/top-level/all-packages.nix2
2 files changed, 32 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix
new file mode 100644
index 0000000000000..0a2074a06e970
--- /dev/null
+++ b/pkgs/applications/science/biology/octopus/default.nix
@@ -0,0 +1,30 @@
+{stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}:
+
+stdenv.mkDerivation rec {
+  pname = "octopus";
+  version = "0.6.3-beta";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "luntergroup";
+    repo = "octopus";
+    rev = "v${version}";
+    sha256 = "042fycg8ppld7iajpzq2d8h8wr0nw43zbl57y125sfihryvr373n";
+  };
+
+  nativeBuildInputs = [ cmake pkg-config ];
+  buildInputs = [ boost gmp htslib zlib lzma ];
+
+  postInstall = ''
+    mkdir $out/bin
+    mv $out/octopus $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Bayesian haplotype-based mutation calling";
+    license = licenses.mit;
+    homepage = "https://github.com/luntergroup/octopus";
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index ace2dd383642d..06d1f946a8325 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -22433,6 +22433,8 @@ in
 
   niftyseg = callPackage ../applications/science/biology/niftyseg { };
 
+  octopus-caller = callPackage ../applications/science/biology/octopus { };
+
   paml = callPackage ../applications/science/biology/paml { };
 
   picard-tools = callPackage ../applications/science/biology/picard-tools { };