From 90b4796c607962bed2ffd8dbe003def02a8c0aa9 Mon Sep 17 00:00:00 2001
From: Bruno Bzeznik <Bruno.Bzeznik@imag.fr>
Date: Wed, 27 Mar 2019 15:20:32 +0100
Subject: [PATCH] sumatools: init at 1.0.34

---
 .../science/biology/sumatools/default.nix     | 65 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  5 ++
 2 files changed, 70 insertions(+)
 create mode 100644 pkgs/applications/science/biology/sumatools/default.nix

diff --git a/pkgs/applications/science/biology/sumatools/default.nix b/pkgs/applications/science/biology/sumatools/default.nix
new file mode 100644
index 00000000000..6f7227d7a3e
--- /dev/null
+++ b/pkgs/applications/science/biology/sumatools/default.nix
@@ -0,0 +1,65 @@
+{ gccStdenv, fetchFromGitLab, zlib }:
+
+let
+  stdenv = gccStdenv;
+  meta = with stdenv.lib; {
+    description = "Fast and exact comparison and clustering of sequences";
+    homepage = https://metabarcoding.org/sumatra;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.unix;
+  };
+
+in rec {
+
+  # Suma library
+  sumalibs = stdenv.mkDerivation rec {
+    version = "1.0.34";
+    pname = "sumalibs";
+    src = fetchFromGitLab {
+      domain = "git.metabarcoding.org";
+      owner = "obitools";
+      repo = pname;
+      rev = "sumalib_v${version}";
+      sha256 = "0hwkrxzfz7m5wdjvmrhkjg8kis378iaqr5n4nhdhkwwhn8x1jn5a";
+    };
+    makeFlags = "PREFIX=$(out)";
+  };
+
+  # Sumatra
+  sumatra = stdenv.mkDerivation rec {
+    version = "1.0.34";
+    pname = "sumatra";
+    src = fetchFromGitLab {
+      domain = "git.metabarcoding.org";
+      owner = "obitools";
+      repo = pname;
+      rev = "${pname}_v${version}";
+      sha256 = "1bbpbdkshdc3xffqnr1qfy8qk64ldsmdc3s8mrcrlx132rgbi5f6";
+    };
+    buildInputs = [ sumalibs zlib ];
+    makeFlags = [
+      "LIBSUMA=${sumalibs}/lib/libsuma.a"
+      "LIBSUMAPATH=-L${sumalibs}"
+      "PREFIX=$(out)"
+    ];
+  };
+
+  # Sumaclust
+  sumaclust = stdenv.mkDerivation rec {
+    version = "1.0.34";
+    pname = "sumaclust";
+    src = fetchFromGitLab {
+      domain = "git.metabarcoding.org";
+      owner = "obitools";
+      repo = pname;
+      rev = "${pname}_v${version}";
+      sha256 = "0x8yi3k3jxhmv2krp4rcjlj2f9zg0qrk7gx4kpclf9c3yxgsgrds";
+    };
+    buildInputs = [ sumalibs ];
+    makeFlags = [
+      "LIBSUMA=${sumalibs}/lib/libsuma.a"
+      "LIBSUMAPATH=-L${sumalibs}"
+      "PREFIX=$(out)"
+    ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 33464ab30a4..a931f7111f9 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21721,6 +21721,11 @@ in
 
   strelka = callPackage ../applications/science/biology/strelka { };
 
+  inherit (callPackages ../applications/science/biology/sumatools {})
+      sumalibs
+      sumaclust
+      sumatra;
+
   seaview = callPackage ../applications/science/biology/seaview { };
 
   varscan = callPackage ../applications/science/biology/varscan { };