diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
8 files changed, 83 insertions, 20 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix b/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix index 64e3f8713b2f..b5b92bd8fe4f 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix @@ -7,8 +7,8 @@ let in stdenv.mkDerivation rec { - srcVersion = "feb23a"; - version = "20230201_a"; + srcVersion = "aug23a"; + version = "20230801_a"; pname = "gildas"; src = fetchurl { @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { # source code of the previous release to a different directory urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.xz" "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.xz" ]; - sha256 = "sha256-A6jtcC8QMtJ7YcNaPiOjwNPDGPAjmRA3jZLEt5iBONE="; + sha256 = "sha256-jlyv2K1V+510C4uLek4oofm13d40nGJ46wqjW+tjfq4="; }; nativeBuildInputs = [ pkg-config groff perl getopt gfortran which ]; @@ -38,14 +38,15 @@ stdenv.mkDerivation rec { echo "gag_doc: $out/share/doc/" >> kernel/etc/gag.dico.lcl ''; + userExec = "astro class greg imager mapping sic"; + postInstall='' mkdir -p $out/bin cp -a ../gildas-exe-${srcVersion}/* $out mv $out/$GAG_EXEC_SYSTEM $out/libexec - cp admin/wrapper.sh $out/bin/gildas-wrapper.sh - chmod 755 $out/bin/gildas-wrapper.sh - for i in $out/libexec/bin/* ; do - ln -s $out/bin/gildas-wrapper.sh $out/bin/$(basename "$i") + for i in ${userExec} ; do + cp admin/wrapper.sh $out/bin/$i + chmod 755 $out/bin/$i done ''; diff --git a/nixpkgs/pkgs/applications/science/biology/bwa-mem2/default.nix b/nixpkgs/pkgs/applications/science/biology/bwa-mem2/default.nix new file mode 100644 index 000000000000..b34b6dc8c90f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bwa-mem2/default.nix @@ -0,0 +1,55 @@ +{ lib +, stdenv +, fetchFromGitHub +, zlib +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "bwa-mem2"; + version = "unstable-2023-03-18"; + + src = fetchFromGitHub { + owner = "bwa-mem2"; + repo = "bwa-mem2"; + rev = "cf4306a47dac35e7e79a9e75398a35f33900cfd0"; + fetchSubmodules = true; + hash = "sha256-1AYSn7nBrDwbX7oSrdEoa1d3t6xzwKnA0S87Y/XeXJg="; + }; + + buildInputs = [ zlib ]; + + # see https://github.com/bwa-mem2/bwa-mem2/issues/93 + postPatch = lib.optionalString stdenv.isDarwin '' + sed -i 's/memset_s/memset8_s/g' ext/safestringlib/include/safe_mem_lib.h + sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset16_s.c + sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset32_s.c + sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset_s.c + sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/wmemset_s.c + ''; + + buildFlags = [ + (if stdenv.hostPlatform.sse4_2Support then "arch=sse42" + else if stdenv.hostPlatform.avxSupport then "arch=avx" + else if stdenv.hostPlatform.avx2Support then "arch=avx2" + else if stdenv.hostPlatform.avx512Support then "arch=avx512" + else "arch=sse41") + ]; + enableParallelBuilding = true; + installPhase = '' + runHook preInstall + + mkdir -p $out/bin + cp bwa-mem2* $out/bin/ + + runHook postInstall + ''; + + meta = with lib; { + description = "Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequences against a large reference genome"; + license = licenses.mit; + homepage = "https://github.com/bwa-mem2/bwa-mem2/"; + changelog = "https://github.com/bwa-mem2/bwa-mem2/blob/${finalAttrs.src.rev}/NEWS.md"; + platforms = platforms.x86_64; + maintainers = with maintainers; [ alxsimon ]; + }; +}) diff --git a/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix index a2ea5b901535..5343f102b249 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "ergoscf"; - version = "3.8"; + version = "3.8.2"; src = fetchurl { url = "http://www.ergoscf.org/source/tarfiles/ergo-${version}.tar.gz"; - sha256 = "1s50k2gfs3y6r5kddifn4p0wmj0yk85wm5vf9v3swm1c0h43riix"; + sha256 = "sha256-U0NVREEZ8HI0Q0ZcbwvZsYA76PWMh7bqgDG1uaUc01c="; }; buildInputs = [ blas lapack ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix b/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix index 14cfac4c1e6e..652a96617cbc 100644 --- a/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix @@ -13,13 +13,13 @@ stdenv.mkDerivation rec { pname = "gerbv"; - version = "2.9.8"; + version = "2.10.0"; src = fetchFromGitHub { owner = "gerbv"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-6r9C5qDOXsQoLsYMSCuIS01gI0ijH7WDoepcowo1yQw="; + hash = "sha256-sr48RGLYcMKuyH9p+5BhnR6QpKBvNOqqtRryw3+pbBk="; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix b/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix index 228027d187bd..9cc88ca7081d 100644 --- a/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cbmc/default.nix @@ -13,13 +13,13 @@ stdenv.mkDerivation rec { pname = "cbmc"; - version = "5.89.0"; + version = "5.90.0"; src = fetchFromGitHub { owner = "diffblue"; repo = pname; rev = "${pname}-${version}"; - sha256 = "sha256-pgZdR1X0aOCfCKAGo2h9bAIO2XTTiWL8ERgandOQj/M="; + sha256 = "sha256-c6Ms/IStmKug5nz37TzjeexkY3YfWaUqEKIC2viMK9g="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix index 1d402573146e..c5e263c319e6 100644 --- a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix @@ -8,13 +8,13 @@ stdenv.mkDerivation rec { pname = "cryptominisat"; - version = "5.11.11"; + version = "5.11.12"; src = fetchFromGitHub { owner = "msoos"; repo = "cryptominisat"; rev = version; - hash = "sha256-TYuOgOOs1EsdNz7ctZMsArTlw3QzHjiPZVozuniiPcI="; + hash = "sha256-1AJx8gPf+qDpAp0p4cfCObKZDWKDAKdGopllr2ajpHw="; }; buildInputs = [ python3 boost ]; diff --git a/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix b/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix index db066ea46317..38b668804ad1 100644 --- a/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix +++ b/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix @@ -1,7 +1,7 @@ { lib, stdenv, unzip, fetchurl, electron, makeWrapper, geogebra }: let pname = "geogebra"; - version = "6-0-785-0"; + version = "6-0-794-0"; srcIcon = geogebra.srcIcon; desktopItem = geogebra.desktopItem; @@ -30,9 +30,9 @@ let src = fetchurl { urls = [ "https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip" - "https://web.archive.org/web/20230627211859/https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip" + "https://web.archive.org/web/20230824011801/https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip" ]; - hash = "sha256-Yv8pTCKkyM7XMUNV2Pcn/YxWo1MbOTNMQBFuJFhB/uE="; + hash = "sha256-sNCq1Xcx/Y5r+SIRiqQYcG9dVsfIC2Ef5KJf+tgfxC8="; }; dontConfigure = true; @@ -65,9 +65,9 @@ let src = fetchurl { urls = [ "https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip" - "https://web.archive.org/web/20230627214413/https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip" + "https://web.archive.org/web/20230824012900/https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip" ]; - hash = "sha256-HtIhhq8E1Q5B6xZ7q6Ok95Rt53VWLoGf8PbY+UEOSKg="; + hash = "sha256-CrSoKAjXiejfJHyv8wIpcRr2d8u/50HnatiDm1CdnGQ="; }; dontUnpack = true; diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix index dee6e8eb0d4b..9fe07603fe7d 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix @@ -103,6 +103,13 @@ stdenv.mkDerivation rec { url = "https://github.com/sagemath/sage/commit/1a1b49f814cdf4c4c8d0ac8930610f3fef6af5b0.diff"; sha256 = "sha256-GqMgoi0tsP7zcCcPumhdsbvhPB6fgw1ufx6gHlc6iSc="; }) + + # https://github.com/sagemath/sage/pull/36006, positively reviewed + (fetchpatch { + name = "gmp-6.3-upgrade.patch"; + url = "https://github.com/sagemath/sage/commit/d88bc3815c0901bfdeaa3e4a31107c084199f614.diff"; + sha256 = "sha256-dXaEwk2wXxmx02sCw4Vu9mF0ZrydhFD4LRwNAiQsPgM="; + }) ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; |