From 05889c52b9cc857ca7f1a286f40b9c9fcb8fe874 Mon Sep 17 00:00:00 2001
From: Renato Alves <alves.rjc@gmail.com>
Date: Fri, 2 Feb 2018 02:24:19 +0100
Subject: [PATCH] RAxML: init at 8.2.11 (SSE3 & MPI)

This can potentially be extended to cover all the other compilation
targets. SSE3-PTHREADS and MPI being the most commonly used.
---
 .../science/biology/raxml/default.nix         | 42 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  6 +++
 2 files changed, 48 insertions(+)
 create mode 100644 pkgs/applications/science/biology/raxml/default.nix

diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix
new file mode 100644
index 000000000000..0bac6c778049
--- /dev/null
+++ b/pkgs/applications/science/biology/raxml/default.nix
@@ -0,0 +1,42 @@
+{ stdenv
+, fetchFromGitHub
+, zlib
+, pkgs
+, mpi ? false
+}:
+
+stdenv.mkDerivation rec {
+  pname = "RAxML";
+  version = "8.2.11";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "stamatak";
+    repo = "standard-${pname}";
+    rev = "v${version}";
+    sha256 = "08fmqrr7y5a2fmmrgfz2p0hmn4mn71l5yspxfcwwsqbw6vmdfkhg";
+  };
+
+  buildInputs = if mpi then [ pkgs.openmpi ] else [];
+
+  # TODO darwin, AVX and AVX2 makefile targets
+  buildPhase = if mpi then ''
+      make -f Makefile.MPI.gcc
+    '' else ''
+      make -f Makefile.SSE3.PTHREADS.gcc
+    '';
+
+  installPhase = if mpi then ''
+    mkdir -p $out/bin && cp raxmlHPC-MPI $out/bin
+  '' else ''
+    mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies";
+    license = licenses.gpl3;
+    homepage = https://sco.h-its.org/exelixis/web/software/raxml/;
+    maintainers = [ maintainers.unode ];
+    platforms = [ "i686-linux" "x86_64-linux" ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 3c5943c54381..cd2c2da4f653 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -19044,6 +19044,12 @@ with pkgs;
 
   plink-ng = callPackage ../applications/science/biology/plink-ng/default.nix { };
 
+  raxml = callPackage ../applications/science/biology/raxml { };
+
+  raxml-mpi = appendToName "mpi" (raxml.override {
+    mpi = true;
+  });
+
   samtools = callPackage ../applications/science/biology/samtools/default.nix { };
 
   snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };