diff options
author | Jonas Heinrich <onny@project-insanity.org> | 2022-08-25 15:25:03 +0200 |
---|---|---|
committer | GitHub <noreply@github.com> | 2022-08-25 15:25:03 +0200 |
commit | 21ba29f2269215a48fd9afc7c52fd9e4e9c432cf (patch) | |
tree | 99fee829cb3199a8112e069094ceb6f5f0a2cc1e | |
parent | fbd067fef00d37b1e168765dbd243df28db274c8 (diff) | |
parent | bb3ed09b06bd4ac113b6192b45f3f993cf28be84 (diff) |
Merge pull request #181338 from thyol/diamond
diamond: 0.8.36 -> 2.0.15
5 files changed, 27 insertions, 41 deletions
diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix index 5bca2dca9f774..2da9655e1599e 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 3b7f4f7ef5dcf..c1b7b096406d6 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 @@ -478,6 +478,14 @@ </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 misunderstood <literal>contents</literal> parameter, in favor of <literal>copyToRoot</literal>. Use diff --git a/nixos/doc/manual/release-notes/rl-2211.section.md b/nixos/doc/manual/release-notes/rl-2211.section.md index 4c4b226b97cff..97775b51c15e3 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 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> |