Merge pull request #24840 from matthiasbeyer/pr-23111-fixed

diamond: init at 0.8.36

pkgs/applications/science/biology/diamond/default.nix

···
+{ stdenv, fetchurl, cmake, gcc, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "diamond-0.8.36";
+
+  src = fetchurl {
+    url = "https://github.com/bbuchfink/diamond/archive/v0.8.36.tar.gz";
+    sha256 = "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh";
+  };
+
+  patches = [
+    ./diamond-0.8.36-no-warning.patch
+  ];
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib ];
+
+  meta = with stdenv.lib; {
+    description = "Accelerated BLAST compatible local sequence aligner";
+    longDescription = ''
+      A sequence aligner for protein and translated DNA
+      searches and functions as a drop-in replacement for the NCBI BLAST
+      software tools. It is suitable for protein-protein search as well as
+      DNA-protein search on short reads and longer sequences including contigs
+      and assemblies, providing a speedup of BLAST ranging up to x20,000.
+
+      DIAMOND is developed by Benjamin Buchfink. Feel free to contact him for support (Email Twitter).
+
+      If you use DIAMOND in published research, please cite
+      B. Buchfink, Xie C., D. Huson,
+      "Fast and sensitive protein alignment using DIAMOND",
+      Nature Methods 12, 59-60 (2015).
+        '';
+    homepage = https://github.com/bbuchfink/diamond;
+    license = {
+      fullName = "University of Tuebingen, Benjamin Buchfink";
+      url = https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING;
+    };
+    maintainers = [ maintainers.metabar ];
+  };
+}

pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch

···
+diff -u -r diamond-0.8.36/src/dp/scalar_traceback.h diamond-0.8.36-patched/src/dp/scalar_traceback.h
+--- diamond-0.8.36/src/dp/scalar_traceback.h	2017-02-06 16:32:05.000000000 +0100
++++ diamond-0.8.36-patched/src/dp/scalar_traceback.h	2017-02-23 15:13:24.000000000 +0100
+@@ -19,6 +19,7 @@
+ #ifndef SCALAR_TRACEBACK_H_
+ #define SCALAR_TRACEBACK_H_
+ 
++#include <cmath>
+ #include <exception>
+ #include "../basic/score_matrix.h"
+ 
+@@ -31,7 +32,7 @@
+ template<>
+ inline bool almost_equal<float>(float x, float y)
+ {
+-	return abs(x - y) < 0.001f;
++	return std::abs(x - y) < 0.001f;
+ }
+ 
+ template<typename _score>

pkgs/top-level/all-packages.nix

···
 
   bcftools = callPackage ../applications/science/biology/bcftools { };
 
+  diamond = callPackage ../applications/science/biology/diamond { };
+
   ecopcr = callPackage ../applications/science/biology/ecopcr { };
 
   emboss = callPackage ../applications/science/biology/emboss { };