diff options
Diffstat (limited to 'pkgs/applications/science/biology')
5 files changed, 25 insertions, 10 deletions
diff --git a/pkgs/applications/science/biology/N3/default.nix b/pkgs/applications/science/biology/N3/default.nix index 2f4aa4ce3927..e7ae8fb3cea3 100644 --- a/pkgs/applications/science/biology/N3/default.nix +++ b/pkgs/applications/science/biology/N3/default.nix @@ -1,6 +1,6 @@ { lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, - libminc, EBTKS }: + libminc, ebtks }: stdenv.mkDerivation rec { pname = "N3"; @@ -13,11 +13,16 @@ stdenv.mkDerivation rec { sha256 = "06hci7gzhy8p34ggvx7gah2k9yxpwhgmq1cgw8pcd1r82g4rg6kd"; }; + postPatch = '' + substituteInPlace src/VolumeHist/DHistogram.cc \ + --replace "register " "" + ''; + nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ libminc EBTKS ]; + buildInputs = [ libminc ebtks ]; propagatedBuildInputs = with perlPackages; [ perl MNI-Perllib GetoptTabular ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${ebtks}/lib/" ]; postFixup = '' for p in $out/bin/*; do diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 827fdb6fa1ab..f7be7119b85d 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "igv"; - version = "2.17.0"; + version = "2.17.1"; src = fetchzip { url = "https://data.broadinstitute.org/igv/projects/downloads/${lib.versions.majorMinor version}/IGV_${version}.zip"; - sha256 = "sha256-nOwaeVIvqfHrvykfTyOdnMN6+QpsvNN14jXBQx7THsE="; + sha256 = "sha256-EXI1jVr8cJPYLLe81hzqLpP3IypHBZ0cb6z+WrDeFKQ="; }; installPhase = '' diff --git a/pkgs/applications/science/biology/inormalize/default.nix b/pkgs/applications/science/biology/inormalize/default.nix index b4999193e177..bf24f0ce19bf 100644 --- a/pkgs/applications/science/biology/inormalize/default.nix +++ b/pkgs/applications/science/biology/inormalize/default.nix @@ -1,6 +1,6 @@ { lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, - libminc, EBTKS }: + libminc, ebtks }: stdenv.mkDerivation rec { pname = "inormalize"; @@ -15,11 +15,16 @@ stdenv.mkDerivation rec { patches = [ ./lgmask-interp.patch ./nu_correct_norm-interp.patch ]; + postPatch = '' + substituteInPlace inormalize.cc \ + --replace "clamp" "::clamp" + ''; + nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ libminc EBTKS ]; + buildInputs = [ libminc ebtks ]; propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${ebtks}/lib/" ]; postFixup = '' for p in $out/bin/*; do diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix index 976dd65ef223..0b0491a71aae 100644 --- a/pkgs/applications/science/biology/spades/default.nix +++ b/pkgs/applications/science/biology/spades/default.nix @@ -17,6 +17,11 @@ stdenv.mkDerivation rec { sourceRoot = "${pname}-${version}/src"; + env.CXXFLAGS = toString [ + # GCC 13: error: 'uint32_t' does not name a type + "-include cstdint" + ]; + meta = with lib; { description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"; license = licenses.gpl2Only; diff --git a/pkgs/applications/science/biology/stacks/default.nix b/pkgs/applications/science/biology/stacks/default.nix index 0a18c5f40fda..3d385b54d469 100644 --- a/pkgs/applications/science/biology/stacks/default.nix +++ b/pkgs/applications/science/biology/stacks/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "stacks"; - version = "2.65"; + version = "2.66"; src = fetchurl { url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz"; - sha256 = "sha256-/9a9PWKVq5yJzEUfOF03zR1Hp3AZw9MF8xICoriV4uo="; + sha256 = "sha256-9pHmcLYMdn9xy3vhlOU42Io/4L61auoncfpZNRPUN/I="; }; buildInputs = [ zlib ]; |