diff options
Diffstat (limited to 'pkgs/applications/science')
5 files changed, 43 insertions, 32 deletions
diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix deleted file mode 100644 index f2825eeb97be..000000000000 --- a/pkgs/applications/science/biology/mosdepth/default.nix +++ /dev/null @@ -1,25 +0,0 @@ -{ lib, nimPackages, fetchFromGitHub, docopt, hts, pcre }: - -nimPackages.buildNimPackage rec { - pname = "mosdepth"; - version = "0.3.5"; - nimBinOnly = true; - - src = fetchFromGitHub { - owner = "brentp"; - repo = "mosdepth"; - rev = "v${version}"; - sha256 = "sha256-tG3J51PS6A0WBCZ+j/Nf7aaukFV+DZJsxpbTbvwu0zc="; - }; - - buildInputs = [ docopt hts pcre ]; - nimFlags = hts.nimFlags ++ [ "--threads:off" ]; - - meta = with lib; { - description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing"; - license = licenses.mit; - homepage = "https://github.com/brentp/mosdepth"; - maintainers = with maintainers; [ jbedo ]; - platforms = platforms.linux; - }; -} diff --git a/pkgs/applications/science/math/mathematica/default.nix b/pkgs/applications/science/math/mathematica/default.nix index 289c9b7b6580..c4cebcd8e29a 100644 --- a/pkgs/applications/science/math/mathematica/default.nix +++ b/pkgs/applications/science/math/mathematica/default.nix @@ -77,7 +77,7 @@ callPackage real-drv { homepage = "http://www.wolfram.com/mathematica/"; license = licenses.unfree; sourceProvenance = with sourceTypes; [ binaryNativeCode ]; - maintainers = with maintainers; [ herberteuler ]; + maintainers = with maintainers; [ herberteuler rafaelrc ]; platforms = [ "x86_64-linux" ]; }; } diff --git a/pkgs/applications/science/math/mathematica/generic.nix b/pkgs/applications/science/math/mathematica/generic.nix index 7cd699e58e3c..5064a3ddbdf4 100644 --- a/pkgs/applications/science/math/mathematica/generic.nix +++ b/pkgs/applications/science/math/mathematica/generic.nix @@ -158,9 +158,10 @@ in stdenv.mkDerivation { # Remove PATH restriction, root and avahi daemon checks, and hostname call sed -i ' - s/^PATH=/# &/ + s/^\s*PATH=/# &/ s/isRoot="false"/# &/ - s/^checkAvahiDaemon$/# &/ + s/^\s*checkAvahiDaemon$/:/ + s/^\s*installBundledInstall$/:/ s/`hostname`/""/ ' MathInstaller diff --git a/pkgs/applications/science/math/mathematica/versions.nix b/pkgs/applications/science/math/mathematica/versions.nix index 2bcce6c58c3d..74422621c7b4 100644 --- a/pkgs/applications/science/math/mathematica/versions.nix +++ b/pkgs/applications/science/math/mathematica/versions.nix @@ -8,6 +8,20 @@ let versions = [ { + version = "13.3.1"; + lang = "en"; + language = "English"; + sha256 = "sha256-0+mYVGiF4Qn3eiLIoINSHVIqT8GtlBPFRYIOF+nHyQo="; + installer = "Mathematica_13.3.1_LINUX.sh"; + } + { + version = "13.3.1"; + lang = "en"; + language = "English"; + sha256 = "sha256-03R4s05fmTcZnlZIMSI6xlLER58MIoccoCr27F8BXOk="; + installer = "Mathematica_13.3.1_BNDL_LINUX.sh"; + } + { version = "13.3.0"; lang = "en"; language = "English"; diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index 2ca47d812bbf..e669562c9cc7 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -1,8 +1,10 @@ { lib, stdenv, fetchurl, cmake, hwloc, fftw, perl, blas, lapack, mpi, cudatoolkit +, plumed , singlePrec ? true , config -, enableMpi ? false , enableCuda ? config.cudaSupport +, enableMpi ? false +, enablePlumed ? false , cpuAcceleration ? null }: @@ -18,20 +20,39 @@ let if stdenv.hostPlatform.system == "aarch64-linux" then "ARM_NEON_ASIMD" else "None"; + source = + if enablePlumed then + { + version = "2023"; + hash = "sha256-rJLG2nL7vMpBT9io2Xnlbs8XxMHNq+0tpc+05yd7e6g="; + } + else + { + version = "2023.3"; + hash = "sha256-Tsj40MevdrE/j9FtuOLBIOdJ3kOa6VVNn2U/gS140cs="; + }; + in stdenv.mkDerivation rec { pname = "gromacs"; - version = "2023.3"; + version = source.version; src = fetchurl { url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz"; - sha256 = "sha256-Tsj40MevdrE/j9FtuOLBIOdJ3kOa6VVNn2U/gS140cs="; + inherit (source) hash; }; patches = [ ./pkgconfig.patch ]; + postPatch = lib.optionalString enablePlumed '' + plumed patch -p -e gromacs-2023 + ''; + outputs = [ "out" "dev" "man" ]; - nativeBuildInputs = [ cmake ]; + nativeBuildInputs = + [ cmake ] + ++ lib.optional enablePlumed plumed + ; buildInputs = [ fftw |