diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index 5bca2dca9f77..2da9655e1599 100644
--- a/maintainers/maintainer-list.nix
+++ b/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";
diff --git a/nixos/doc/manual/from_md/release-notes/rl-2211.section.xml b/nixos/doc/manual/from_md/release-notes/rl-2211.section.xml
index 3b7f4f7ef5dc..c1b7b096406d 100644
--- a/nixos/doc/manual/from_md/release-notes/rl-2211.section.xml
+++ b/nixos/doc/manual/from_md/release-notes/rl-2211.section.xml
@@ -476,6 +476,14 @@
and require manual remediation.
+
+
+ The diamond package has been update from
+ 0.8.36 to 2.0.15. See the
+ upstream
+ release notes for more details.
+
+ dockerTools.buildImage deprecates the
diff --git a/nixos/doc/manual/release-notes/rl-2211.section.md b/nixos/doc/manual/release-notes/rl-2211.section.md
index 4c4b226b97cf..97775b51c15e 100644
--- a/nixos/doc/manual/release-notes/rl-2211.section.md
+++ b/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`.
diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix
index 86b239c93843..8073b1bea163 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 a16d475c5564..000000000000
--- 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
- #include
- #include "../basic/score_matrix.h"
-
-@@ -31,7 +32,7 @@
- template<>
- inline bool almost_equal(float x, float y)
- {
-- return abs(x - y) < 0.001f;
-+ return std::abs(x - y) < 0.001f;
- }
-
- template