diff options
Diffstat (limited to 'pkgs/applications/science')
5 files changed, 5 insertions, 59 deletions
diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix index 400e073f69057..56cfa5168a486 100644 --- a/pkgs/applications/science/biology/kent/default.nix +++ b/pkgs/applications/science/biology/kent/default.nix @@ -13,13 +13,13 @@ }: stdenv.mkDerivation rec { pname = "kent"; - version = "465"; + version = "466"; src = fetchFromGitHub { owner = "ucscGenomeBrowser"; repo = pname; rev = "v${version}_base"; - hash = "sha256-QeHqXSbad5LCmQ8DfLxl2pyXJvKV4G7uLXBtRd7LME0="; + hash = "sha256-zoDZ+8G0SHKfWmkXBqp+WSjQXtmkcTIZjrjPhUIJw1c="; }; buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; diff --git a/pkgs/applications/science/biology/poretools/default.nix b/pkgs/applications/science/biology/poretools/default.nix deleted file mode 100644 index 27a1b7ed38416..0000000000000 --- a/pkgs/applications/science/biology/poretools/default.nix +++ /dev/null @@ -1,23 +0,0 @@ -{ lib, python2Packages, fetchFromGitHub }: - -python2Packages.buildPythonPackage rec { - pname = "poretools"; - version = "unstable-2016-07-10"; - - src = fetchFromGitHub { - repo = pname; - owner = "arq5x"; - rev = "e426b1f09e86ac259a00c261c79df91510777407"; - sha256 = "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"; - }; - - propagatedBuildInputs = [ python2Packages.h5py python2Packages.matplotlib python2Packages.seaborn python2Packages.pandas ]; - - meta = { - description = "Toolkit for working with nanopore sequencing data from Oxford Nanopore"; - license = lib.licenses.mit; - homepage = "https://poretools.readthedocs.io/en/latest/"; - maintainers = [ lib.maintainers.rybern ]; - broken = true; # Build error: h5py-3.9.0 not supported for interpreter python2.7 - }; -} diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix deleted file mode 100644 index 0b0491a71aaef..0000000000000 --- a/pkgs/applications/science/biology/spades/default.nix +++ /dev/null @@ -1,32 +0,0 @@ -{ lib, stdenv, fetchurl, zlib, bzip2, cmake, python3 }: - -stdenv.mkDerivation rec { - pname = "SPAdes"; - version = "3.15.5"; - - src = fetchurl { - url = "http://cab.spbu.ru/files/release${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/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 68b424b32fb4a..af672d500fa6a 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -58,6 +58,7 @@ let "8.18.0".sha256 = "sha256-WhiBs4nzPHQ0R24xAdM49kmxSCPOxiOVMA1iiMYunz4="; "8.19.0".sha256 = "sha256-ixsYCvCXpBHqJ71hLQklphlwoOO3i/6w2PJjllKqf9k="; "8.19.1".sha256 = "sha256-kmZ8Uk8jpzjOd67aAPp3C+vU2oNaBw9pr7+Uixcgg94="; + "8.19.2".sha256 = "sha256-q+i07JsMZp83Gqav6v1jxsgPLN7sPvp5/oszVnavmz0="; }; releaseRev = v: "V${v}"; fetched = import ../../../../build-support/coq/meta-fetch/default.nix diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index ade5239762518..7f0e70c642134 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -6,14 +6,14 @@ python3.pkgs.buildPythonApplication rec { pname = "snakemake"; - version = "8.13.0"; + version = "8.14.0"; format = "setuptools"; src = fetchFromGitHub { owner = "snakemake"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-Xd8mZ8tsemJ53hAMED2biRyDlEw/gG/Hh1iZSwSB1vY="; + hash = "sha256-6oguN4u4OUDXpDsbueSBNwtWgLCaKmgq3w/d/MsMh7Y="; # https://github.com/python-versioneer/python-versioneer/issues/217 postFetch = '' sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#' |