Merge pull request #181338 from thyol/diamond

diamond: 0.8.36 -> 2.0.15

maintainers/maintainer-list.nix

@@ -13055,6 +13055,12 @@
     githubId = 3268082;
     name = "Thibaut Marty";
   };
+  thyol = {
+    name = "thyol";
+    email = "thyol@pm.me";
+    github = "thyol";
+    githubId = 81481634;
+  };
   thmzlt = {
     email = "git@thomazleite.com";
     github = "thmzlt";

nixos/doc/manual/from_md/release-notes/rl-2211.section.xml

@@ -476,6 +476,14 @@
           and require manual remediation.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          The <literal>diamond</literal> package has been update from
+          0.8.36 to 2.0.15. See the
+          <link xlink:href="https://github.com/bbuchfink/diamond/releases">upstream
+          release notes</link> for more details.
+        </para>
+      </listitem>
       <listitem>
         <para>
           <literal>dockerTools.buildImage</literal> deprecates the

nixos/doc/manual/release-notes/rl-2211.section.md

@@ -164,6 +164,8 @@ Use `configure.packages` instead.
 
 - Matrix Synapse now requires entries in the `state_group_edges` table to be unique, in order to prevent accidentally introducing duplicate information (for example, because a database backup was restored multiple times). If your Synapse database already has duplicate rows in this table, this could fail with an error and require manual remediation.
 
+- The `diamond` package has been update from 0.8.36 to 2.0.15. See the [upstream release notes](https://github.com/bbuchfink/diamond/releases) for more details.
+
 - `dockerTools.buildImage` deprecates the misunderstood `contents` parameter, in favor of `copyToRoot`.
   Use `copyToRoot = buildEnv { ... };` or similar if you intend to add packages to `/bin`.
 

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 ];
   };
 }

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

@@ -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>