Merge pull request #181338 from thyol/diamond

diamond: 0.8.36 -> 2.0.15

2 files changed, 11 insertions, 41 deletions

diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix
index 86b239c93843e..8073b1bea1634 100644
--- a/pkgs/applications/science/biology/diamond/default.nix
+++ b/pkgs/applications/science/biology/diamond/default.nix
@@ -2,18 +2,15 @@
 
 stdenv.mkDerivation rec {
   pname = "diamond";
-  version = "0.8.36";
+  version = "2.0.15";
 
   src = fetchFromGitHub {
     owner = "bbuchfink";
     repo = "diamond";
     rev = "v${version}";
-    sha256 = "sha256-7uqOQOzkYN0RNwKBGUZ/Ny5NVZMoGByOk+GUvjdBzck=";
+    sha256 = "17z9vwj58i1zc22gv4qscx0dk3nxf5ix443gxsibh3a5zsnc6dkg";
   };
 
-  patches = [
-    ./diamond-0.8.36-no-warning.patch
-  ];
 
   nativeBuildInputs = [ cmake ];
   buildInputs = [ zlib ];
@@ -21,24 +18,17 @@ stdenv.mkDerivation rec {
   meta = with 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 a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:
+      - Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST.
+      - Frameshift alignments for long read analysis.
+      - Low resource requirements and suitable for running on standard desktops or laptops.
+      - Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.
 
-      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).
+      When using the tool in published research, please cite:
+      - Buchfink B, Reuter K, Drost HG, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nature Methods 18, 366–368 (2021). doi:10.1038/s41592-021-01101-x
     '';
     homepage = "https://github.com/bbuchfink/diamond";
-    license = {
-      fullName = "University of Tuebingen, Benjamin Buchfink";
-      url = "https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING";
-    };
-    maintainers = [ ];
+    license = lib.licenses.gpl3Plus;
+    maintainers = with lib.maintainers; [ thyol ];
   };
 }
diff --git a/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch b/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch
deleted file mode 100644
index a16d475c5564f..0000000000000
--- a/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-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>