diff options
Diffstat (limited to 'pkgs/applications/science')
14 files changed, 87 insertions, 26 deletions
diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index eb7ba2a8c9c47..fb7963416167d 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -6,13 +6,13 @@ mkDerivation rec { name = "stellarium-${version}"; - version = "0.18.3"; + version = "0.19.0"; src = fetchFromGitHub { owner = "Stellarium"; repo = "stellarium"; rev = "v${version}"; - sha256 = "1cnwfk3vdsxh8gacw22qik401z0kpzd1ralbg9ph2cjqx9x2m1s1"; + sha256 = "1x9s9v9ann93nyqd8n8adwhx66xgq5vp0liyzl1h1ji6qk8jla3c"; }; nativeBuildInputs = [ cmake perl ]; diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix index e97b5d1a3f4fc..516608466a932 100644 --- a/pkgs/applications/science/biology/bowtie2/default.nix +++ b/pkgs/applications/science/biology/bowtie2/default.nix @@ -2,14 +2,14 @@ stdenv.mkDerivation rec { pname = "bowtie2"; - version = "2.3.4.3"; + version = "2.3.5"; name = "${pname}-${version}"; src = fetchFromGitHub { owner = "BenLangmead"; repo = pname; rev = "v${version}"; - sha256 = "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"; + sha256 = "12v240wnbc541hl4z2fiymxd3bd6czazs13fjkygldflg48w45m0"; }; buildInputs = [ zlib tbb python perl ]; diff --git a/pkgs/applications/science/biology/itsx/default.nix b/pkgs/applications/science/biology/itsx/default.nix new file mode 100644 index 0000000000000..804e71c1bfa7d --- /dev/null +++ b/pkgs/applications/science/biology/itsx/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchurl, hmmer, perl }: + +stdenv.mkDerivation rec { + version = "1.1.1"; + name = "itsx-${version}"; + + src = fetchurl { + url = "http://microbiology.se/sw/ITSx_${version}.tar.gz"; + sha256 = "0lrmy2n3ax7f208k0k8l3yz0j5cpz05hv4hx1nnxzn0c51z1pc31"; + }; + + buildInputs = [ hmmer perl ]; + + buildPhase = '' + sed -e "s,profileDB = .*,profileDB = \"$out/share/ITSx_db/HMMs\";," -i ITSx + sed "3 a \$ENV{\'PATH\'}='${hmmer}/bin:'.\"\$ENV{\'PATH\'}\";" -i ITSx + mkdir bin + mv ITSx bin + ''; + + installPhase = '' + mkdir -p $out/share/doc && cp -a bin $out/ + cp *pdf $out/share/doc + cp -r ITSx_db $out/share + ''; + + meta = with stdenv.lib; { + description = "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing"; + homepage = http://microbiology.se/software/itsx/; + license = licenses.gpl3; + maintainers = [ maintainers.bzizou ]; + platforms = [ "x86_64-linux" "i686-linux" ]; + }; +} diff --git a/pkgs/applications/science/biology/messer-slim/default.nix b/pkgs/applications/science/biology/messer-slim/default.nix new file mode 100644 index 0000000000000..dbbf8d39a93c1 --- /dev/null +++ b/pkgs/applications/science/biology/messer-slim/default.nix @@ -0,0 +1,27 @@ +{ stdenv, fetchurl, cmake, gcc, gcc-unwrapped }: + +stdenv.mkDerivation rec { + version = "3.2.1"; + name = "messer-slim-${version}"; + + src = fetchurl { + url = "https://github.com/MesserLab/SLiM/archive/v${version}.tar.gz"; + sha256 = "1j3ssjvxpsc21mmzj59kwimglz8pdazi5w6wplmx11x744k77wa1"; + }; + + enableParallelBuilding = true; + + nativeBuildInputs = [ cmake gcc gcc-unwrapped ]; + + cmakeFlags = [ "-DCMAKE_AR=${gcc-unwrapped}/bin/gcc-ar" + "-DCMAKE_RANLIB=${gcc-unwrapped}/bin/gcc-ranlib" ]; + + meta = { + description = "An evolutionary simulation framework"; + homepage = https://messerlab.org/slim/; + license = with stdenv.lib.licenses; [ gpl3 ]; + maintainers = with stdenv.lib.maintainers; [ bzizou ]; + platforms = stdenv.lib.platforms.all; + }; +} + diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index 3f28b5e31ccd2..85c2b99b3a78d 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -3,13 +3,13 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "minimap2"; - version = "2.15"; + version = "2.16"; src = fetchFromGitHub { repo = pname; owner = "lh3"; rev = "v${version}"; - sha256 = "0dy3m2wjmi3whjnmkj3maa1aadz525h7736wm8vvdcwq71ijqb7v"; + sha256 = "1ggm5psv3gwsz627ik9kl6ry9gzgmfsvya6ni0gv6ahwlrhdim73"; }; buildInputs = [ zlib ]; diff --git a/pkgs/applications/science/biology/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix index fe25a04c420ae..68efc2030e533 100644 --- a/pkgs/applications/science/biology/paml/default.nix +++ b/pkgs/applications/science/biology/paml/default.nix @@ -1,11 +1,11 @@ {stdenv, fetchurl}: stdenv.mkDerivation rec { - version = "4.9h"; + version = "4.9i"; name = "paml-${version}"; src = fetchurl { url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz"; - sha256 = "1czdfb3naadq0d3y42isrbyja33c3p28k8dv9mxlx2h19b7zcfv2"; + sha256 = "1k5lcyls6c33ppp5fxl8ply2fy7i2k0gcqaifsl7gnc81d8ay4dw"; }; preBuild = '' diff --git a/pkgs/applications/science/chemistry/molden/default.nix b/pkgs/applications/science/chemistry/molden/default.nix index 99a8c777cd0ea..35d21848e2b3f 100644 --- a/pkgs/applications/science/chemistry/molden/default.nix +++ b/pkgs/applications/science/chemistry/molden/default.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl, which, gfortran, libGLU, xorg } : stdenv.mkDerivation rec { - version = "5.9.3"; + version = "5.9.5"; name = "molden-${version}"; src = fetchurl { url = "ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden${version}.tar.gz"; - sha256 = "18fz44g7zkm0xcx3w9hm049jv13af67ww7mb5b3kdhmza333a16q"; + sha256 = "0va5g03kvnzydx0b77y1p536iy7swzvnx6yknp87qgpw1bgrzdj9"; }; nativeBuildInputs = [ which ]; diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix index 2dd3c9b64c439..5fc71c9fc6baf 100644 --- a/pkgs/applications/science/chemistry/octopus/default.nix +++ b/pkgs/applications/science/chemistry/octopus/default.nix @@ -3,7 +3,7 @@ }: let - version = "8.3"; + version = "8.4"; fftwAll = symlinkJoin { name ="ftw-dev-out"; paths = [ fftw.dev fftw.out ]; }; in stdenv.mkDerivation { @@ -11,7 +11,7 @@ in stdenv.mkDerivation { src = fetchurl { url = "http://www.tddft.org/programs/octopus/down.php?file=${version}/octopus-${version}.tar.gz"; - sha256 = "0nr3qmyfhp6fy8qrp4p43pl5xxfqgqg5g1c2775hxhpsi29xr7zf"; + sha256 = "1fx5ssnf65b9ld7xs9rvvg8i80pblxpyhqkir0a7xshkk1g60z55"; }; nativeBuildInputs = [ perl procps fftw.dev ]; diff --git a/pkgs/applications/science/electronics/eagle/eagle.nix b/pkgs/applications/science/electronics/eagle/eagle.nix index b97ede4139631..831ec9662b098 100644 --- a/pkgs/applications/science/electronics/eagle/eagle.nix +++ b/pkgs/applications/science/electronics/eagle/eagle.nix @@ -13,11 +13,11 @@ let in stdenv.mkDerivation rec { name = "eagle-${version}"; - version = "9.1.2"; + version = "9.3.1"; src = fetchurl { url = "https://eagle-updates.circuits.io/downloads/${builtins.replaceStrings ["."] ["_"] version}/Autodesk_EAGLE_${version}_English_Linux_64bit.tar.gz"; - sha256 = "0y7ahl9z5a7l9cjk8hzmyv6ga8chlry5rr8v116q5mnsgs4i11an"; + sha256 = "0hrbw368kskjzwjnqrri5j7c10d0z5m81h3s9zhqfrmwym42vdc5"; }; desktopItem = makeDesktopItem { diff --git a/pkgs/applications/science/logic/elan/default.nix b/pkgs/applications/science/logic/elan/default.nix index 693aaa53001bc..eddc4b9b20805 100644 --- a/pkgs/applications/science/logic/elan/default.nix +++ b/pkgs/applications/science/logic/elan/default.nix @@ -2,7 +2,7 @@ rustPlatform.buildRustPackage rec { name = "elan-${version}"; - version = "0.7.4"; + version = "0.7.5"; cargoSha256 = "0vv7kr7rc3lvas7ngp5dp99ajjd5v8k5937ish7zqz1k4970q2f1"; @@ -10,7 +10,7 @@ rustPlatform.buildRustPackage rec { owner = "kha"; repo = "elan"; rev = "v${version}"; - sha256 = "0yf8mfgp4l78f5cjq1imh462axaa24jfhn69cgf7prw4jrmw3bch"; + sha256 = "1147f3lzr6lgvf580ppspn20bdwnf6l8idh1h5ana0p0lf5a0dn1"; }; nativeBuildInputs = [ pkgconfig ]; diff --git a/pkgs/applications/science/math/ginac/default.nix b/pkgs/applications/science/math/ginac/default.nix index 18a5281bebb0d..4b9f15e0a92f5 100644 --- a/pkgs/applications/science/math/ginac/default.nix +++ b/pkgs/applications/science/math/ginac/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, cln, pkgconfig, readline, gmp, python }: stdenv.mkDerivation rec { - name = "ginac-1.7.4"; + name = "ginac-1.7.5"; src = fetchurl { url = "${meta.homepage}/${name}.tar.bz2"; - sha256 = "1vvqv73yk9klbq0mz239zzw77rlp72qcvzci4j1v6rafvji1616n"; + sha256 = "11v8dpdfq8ybbbadyakp19xc7jgckplbbj6q2hh1c2hj5ps6njz7"; }; propagatedBuildInputs = [ cln ]; diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index e3760533edae3..8f96eb8f3060b 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg , zlib, libGLU_combined, libGLU, xorg }: -let version = "4.2.1"; in +let version = "4.2.2"; in stdenv.mkDerivation { name = "gmsh-${version}"; src = fetchurl { url = "http://gmsh.info/src/gmsh-${version}-source.tgz"; - sha256 = "1f11481e68900dc256f88aaed18d03e93b416ba01e9e8c3dc3f6d59a211f0561"; + sha256 = "e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc"; }; buildInputs = [ cmake openblasCompat gmm fltk libjpeg zlib libGLU_combined diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index 5104d1012b2fa..61ebed8968755 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchFromGitHub, intltool, autoreconfHook, pkgconfig, libqalculate, gtk3, wrapGAppsHook }: stdenv.mkDerivation rec { - name = "qalculate-gtk-${version}"; - version = "2.9.0"; + pname = "qalculate-gtk"; + version = "3.0.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "0c5s7mz8xwwmzc22yai8vqiww7paafkyi7khp8a2yws78m2nirdx"; + sha256 = "00q6y9dgg9wgpgks79snbipn8alfjajlx02a5hm7wl9a20zd0b81"; }; patchPhase = '' diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index a682d59ab23ae..f0ac310ea6655 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -8,11 +8,11 @@ stdenv.mkDerivation { - name = "gromacs-2019"; + name = "gromacs-2019.1"; src = fetchurl { - url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.tar.gz"; - sha256 = "02qd27pgc5kwkk68m8hwarkbb1b9z5rdrm67yjqyxd5my2jq3cn5"; + url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.1.tar.gz"; + sha256 = "1v438nf6viwpl53ydrljf598cf8lh7jqxp5bzi74rrnhzk97xhxj"; }; buildInputs = [cmake fftw] |