diff options
Diffstat (limited to 'pkgs')
-rw-r--r-- | pkgs/applications/science/biology/spades/default.nix | 32 | ||||
-rw-r--r-- | pkgs/by-name/sp/spades/package.nix | 46 | ||||
-rw-r--r-- | pkgs/top-level/aliases.nix | 1 | ||||
-rw-r--r-- | pkgs/top-level/all-packages.nix | 2 |
4 files changed, 47 insertions, 34 deletions
diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix deleted file mode 100644 index 0b0491a71aaef..0000000000000 --- a/pkgs/applications/science/biology/spades/default.nix +++ /dev/null @@ -1,32 +0,0 @@ -{ lib, stdenv, fetchurl, zlib, bzip2, cmake, python3 }: - -stdenv.mkDerivation rec { - pname = "SPAdes"; - version = "3.15.5"; - - src = fetchurl { - url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o="; - }; - - nativeBuildInputs = [ cmake ]; - - buildInputs = [ zlib bzip2 python3 ]; - - doCheck = true; - - sourceRoot = "${pname}-${version}/src"; - - env.CXXFLAGS = toString [ - # GCC 13: error: 'uint32_t' does not name a type - "-include cstdint" - ]; - - meta = with lib; { - description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"; - license = licenses.gpl2Only; - homepage = "http://cab.spbu.ru/software/spades/"; - platforms = [ "x86_64-linux" "x86_64-darwin" ]; - maintainers = [ maintainers.bzizou ]; - }; -} diff --git a/pkgs/by-name/sp/spades/package.nix b/pkgs/by-name/sp/spades/package.nix new file mode 100644 index 0000000000000..9a60ee499a645 --- /dev/null +++ b/pkgs/by-name/sp/spades/package.nix @@ -0,0 +1,46 @@ +{ + lib, + stdenv, + fetchurl, + zlib, + bzip2, + cmake, + python3, +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "spades"; + version = "3.15.5"; + + src = fetchurl { + url = "https://github.com/ablab/spades/releases/download/v${finalAttrs.version}/SPAdes-${finalAttrs.version}.tar.gz"; + hash = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o="; + }; + sourceRoot = "SPAdes-${finalAttrs.version}/src"; + + env.CXXFLAGS = toString [ + # GCC 13: error: 'uint32_t' does not name a type + "-include cstdint" + ]; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ + zlib + bzip2 + python3 + ]; + + doCheck = true; + + meta = { + description = "St. Petersburg genome assembler, a toolkit for assembling and analyzing sequencing data"; + license = lib.licenses.gpl2Only; + homepage = "http://ablab.github.io/spades"; + platforms = [ + "x86_64-linux" + "x86_64-darwin" + ]; + maintainers = with lib.maintainers; [ bzizou ]; + }; +}) diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix index e9f8411186619..213afdf99d9a1 100644 --- a/pkgs/top-level/aliases.nix +++ b/pkgs/top-level/aliases.nix @@ -1228,6 +1228,7 @@ mapAliases ({ solr = throw "'solr' has been removed from nixpkgs, as it was broken and unmaintained"; # Added 2023-03-16 soundOfSorting = sound-of-sorting; # Added 2023-07-07 soundux = throw "'soundux' has been removed, as it is unmaintained."; # Added on 2024-02-14 + SPAdes = spades; # Added 2024-06-12 spark2 = throw "'spark2' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08 spark_2_4 = throw "'spark_2_4' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08 spark_3_1 = throw "'spark_3_1' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08 diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 23771687ef525..4a867078fdbf9 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -37945,8 +37945,6 @@ with pkgs; seaview = callPackage ../applications/science/biology/seaview { }; - SPAdes = callPackage ../applications/science/biology/spades { }; - svaba = callPackage ../applications/science/biology/svaba { }; tandem-aligner = callPackage ../applications/science/biology/tandem-aligner { }; |