diff options
Diffstat (limited to 'pkgs/applications/science')
10 files changed, 98 insertions, 29 deletions
diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix new file mode 100644 index 00000000000..0bac6c77804 --- /dev/null +++ b/pkgs/applications/science/biology/raxml/default.nix @@ -0,0 +1,42 @@ +{ stdenv +, fetchFromGitHub +, zlib +, pkgs +, mpi ? false +}: + +stdenv.mkDerivation rec { + pname = "RAxML"; + version = "8.2.11"; + name = "${pname}-${version}"; + + src = fetchFromGitHub { + owner = "stamatak"; + repo = "standard-${pname}"; + rev = "v${version}"; + sha256 = "08fmqrr7y5a2fmmrgfz2p0hmn4mn71l5yspxfcwwsqbw6vmdfkhg"; + }; + + buildInputs = if mpi then [ pkgs.openmpi ] else []; + + # TODO darwin, AVX and AVX2 makefile targets + buildPhase = if mpi then '' + make -f Makefile.MPI.gcc + '' else '' + make -f Makefile.SSE3.PTHREADS.gcc + ''; + + installPhase = if mpi then '' + mkdir -p $out/bin && cp raxmlHPC-MPI $out/bin + '' else '' + mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin + ''; + + meta = with stdenv.lib; { + description = "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies"; + license = licenses.gpl3; + homepage = https://sco.h-its.org/exelixis/web/software/raxml/; + maintainers = [ maintainers.unode ]; + platforms = [ "i686-linux" "x86_64-linux" ]; + }; +} diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index 640f32671bb..365057414e9 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "samtools"; - version = "1.6"; + version = "1.7"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2"; - sha256 = "17p4vdj2j2qr3b2c0v4100h6cg4jj3zrb4dmdnd9d9aqs74d4p7f"; + sha256 = "e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1"; }; nativeBuildInputs = [ perl ]; diff --git a/pkgs/applications/science/electronics/bitscope/common.nix b/pkgs/applications/science/electronics/bitscope/common.nix index 90bf4dc840d..e1db7131a65 100644 --- a/pkgs/applications/science/electronics/bitscope/common.nix +++ b/pkgs/applications/science/electronics/bitscope/common.nix @@ -65,6 +65,6 @@ let runScript = target; }; in buildFHSUserEnv { - name = attrs.toolName; + name = "${attrs.toolName}-${attrs.version}"; runScript = "${pkg.outPath}/bin/${attrs.toolName}"; } // { inherit (pkg) meta name; } diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix index b3f0b325927..095aa5a7f8c 100644 --- a/pkgs/applications/science/logic/lean/default.nix +++ b/pkgs/applications/science/logic/lean/default.nix @@ -11,7 +11,8 @@ stdenv.mkDerivation rec { sha256 = "0irh9b4haz0pzzxrb4hwcss91a0xb499kjrcrmr2s59p3zq8bbd9"; }; - buildInputs = [ gmp cmake ]; + nativeBuildInputs = [ cmake ]; + buildInputs = [ gmp ]; enableParallelBuilding = true; preConfigure = '' diff --git a/pkgs/applications/science/logic/symbiyosys/default.nix b/pkgs/applications/science/logic/symbiyosys/default.nix index 6a26ee6e3d6..e8feaa0acc4 100644 --- a/pkgs/applications/science/logic/symbiyosys/default.nix +++ b/pkgs/applications/science/logic/symbiyosys/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "symbiyosys-${version}"; - version = "2018.01.10"; + version = "2018.02.04"; src = fetchFromGitHub { - owner = "cliffordwolf"; + owner = "yosyshq"; repo = "symbiyosys"; - rev = "25936009bbc2cffd289c607ddf42a578527aa59c"; - sha256 = "06idd8vbn4s2k6bja4f6lxjc4qwgbak2fhfxj8f18ki1xb3yqfh6"; + rev = "236f6412c1c1afe95d752eaf907f66f19c343134"; + sha256 = "06bsvvkn9yhz9jvgf7a6pf407ab9m5qrr42niww666z967xdw4p0"; }; buildInputs = [ python3 yosys ]; diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index 725b3f342c3..7bd19cfc520 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -1,7 +1,7 @@ { stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng , libtiff, ncurses, pango, pcre, perl, readline, tcl, texLive, tk, xz, zlib , less, texinfo, graphviz, icu, pkgconfig, bison, imake, which, jdk, openblas -, curl, Cocoa, Foundation, cf-private, libobjc, tzdata, fetchpatch +, curl, Cocoa, Foundation, cf-private, libobjc, libcxx, tzdata, fetchpatch , withRecommendedPackages ? true , enableStrictBarrier ? false }: @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { pango pcre perl readline texLive xz zlib less texinfo graphviz icu pkgconfig bison imake which jdk openblas curl ] ++ stdenv.lib.optionals (!stdenv.isDarwin) [ tcl tk ] - ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc ]; + ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ]; patches = [ ./no-usr-local-search-paths.patch ]; @@ -55,6 +55,8 @@ stdenv.mkDerivation rec { --without-aqua --disable-R-framework OBJC="clang" + CPPFLAGS="-isystem ${libcxx}/include/c++/v1" + LDFLAGS="-L${libcxx}/lib" '' + '' ) echo >>etc/Renviron.in "TCLLIBPATH=${tk}/lib" diff --git a/pkgs/applications/science/math/sage/spkg-giac.patch b/pkgs/applications/science/math/sage/spkg-giac.patch index 15b91433d25..c79d4422133 100644 --- a/pkgs/applications/science/math/sage/spkg-giac.patch +++ b/pkgs/applications/science/math/sage/spkg-giac.patch @@ -1,10 +1,19 @@ ---- old/build/pkgs/giac/spkg-install 2017-07-21 14:10:00.000000000 -0500 -+++ new/build/pkgs/giac/spkg-install 2017-10-15 15:55:55.321237645 -0500 -@@ -4,6 +4,8 @@ +diff --git a/build/pkgs/giac/spkg-install b/build/pkgs/giac/spkg-install +index bdd8df6cb8..3fd7a3ef8a 100644 +--- a/build/pkgs/giac/spkg-install ++++ b/build/pkgs/giac/spkg-install +@@ -2,6 +2,15 @@ ## Giac ########################################### -+find . -type f -exec sed -e 's@/bin/cp@cp@g' -i '{}' ';' && echo "Patching input parser" && find . -iname 'input_parser.cc' ++# Fix hardcoded paths, while making sure to only update timestamps of actually ++# changed files (otherwise confuses make) ++grep -rlF '/bin/cp' . | while read file ++do ++ sed -e 's@/bin/cp@cp@g' -i "$file" ++done ++ ++# Fix input parser syntax +sed -e 's@yylex (&yylval)@yylex (\&yyval, scanner)@gp' -i 'src/src/input_parser.cc' if [ "$SAGE_LOCAL" = "" ]; then diff --git a/pkgs/applications/science/math/sage/spkg-git.patch b/pkgs/applications/science/math/sage/spkg-git.patch index ff9a7b2e491..74f552dd3c3 100644 --- a/pkgs/applications/science/math/sage/spkg-git.patch +++ b/pkgs/applications/science/math/sage/spkg-git.patch @@ -1,12 +1,17 @@ diff --git a/build/pkgs/git/spkg-install b/build/pkgs/git/spkg-install -index 8469cb58c2..d0dc9a1db9 100755 +index 87874de3d8..b0906245fa 100644 --- a/build/pkgs/git/spkg-install +++ b/build/pkgs/git/spkg-install -@@ -35,6 +35,8 @@ fi +@@ -33,6 +33,13 @@ fi cd src -+find . -type f -exec sed -e 's@/usr/bin/perl@perl@g' -i '{}' ';' ++# Fix hardcoded paths, while making sure to only update timestamps of actually ++# changed files (otherwise confuses make) ++grep -rlF '/usr/bin/perl' . | while read file ++do ++ sed -e 's@/usr/bin/perl@perl@g' -i "$file" ++done + # We don't want to think about Fink or Macports export NO_FINK=1 diff --git a/pkgs/applications/science/math/sage/spkg-singular.patch b/pkgs/applications/science/math/sage/spkg-singular.patch index d561768600b..606ffcd3ad4 100644 --- a/pkgs/applications/science/math/sage/spkg-singular.patch +++ b/pkgs/applications/science/math/sage/spkg-singular.patch @@ -1,11 +1,17 @@ ---- old/build/pkgs/singular/spkg-install 2017-10-15 10:35:41.826540964 -0500 -+++ new/build/pkgs/singular/spkg-install 2017-10-15 10:36:40.613743443 -0500 -@@ -4,6 +4,9 @@ +diff --git a/build/pkgs/singular/spkg-install b/build/pkgs/singular/spkg-install +index 8caafb1699..3c34e6608a 100644 +--- a/build/pkgs/singular/spkg-install ++++ b/build/pkgs/singular/spkg-install +@@ -2,6 +2,13 @@ ## Singular ########################################### -+find . -type f -exec sed -e 's@/bin/rm@rm@g' -i '{}' ';' -+#echo '#!/usr/bin/env bash\nIgnoring missing $1' > src/build-aux/missing ++# Fix hardcoded paths, while making sure to only update timestamps of actually ++# changed files (otherwise confuses make) ++grep -rlF '/bin/rm' . | while read file ++do ++ sed -e 's@/bin/rm@rm@g' -i "$file" ++done + if [ -z "$SAGE_LOCAL" ]; then echo >&2 "Error: SAGE_LOCAL undefined -- exiting..." diff --git a/pkgs/applications/science/spyder/default.nix b/pkgs/applications/science/spyder/default.nix index 0952b61551e..04a5def81e6 100644 --- a/pkgs/applications/science/spyder/default.nix +++ b/pkgs/applications/science/spyder/default.nix @@ -1,7 +1,7 @@ { stdenv, fetchPypi, unzip, buildPythonApplication, makeDesktopItem # mandatory -, qtpy, numpydoc, qtconsole, qtawesome, jedi, pycodestyle, psutil -, pyflakes, rope, sphinx, nbconvert, mccabe +, numpydoc, qtconsole, qtawesome, jedi, pycodestyle, psutil +, pyflakes, rope, sphinx, nbconvert, mccabe, pyopengl, cloudpickle # optional , numpy ? null, scipy ? null, matplotlib ? null # optional @@ -10,17 +10,21 @@ buildPythonApplication rec { pname = "spyder"; - version = "3.2.4"; - namePrefix = ""; + version = "3.2.6"; src = fetchPypi { inherit pname version; - sha256 = "028hg71gfq2yrplwhhl7hl4rbwji1l0zxzghblwmb0i443ki10v3"; + sha256 = "87d6a4f5ee1aac4284461ee3584c3ade50cb53feb3fe35abebfdfb9be18c526a"; }; + # Somehow setuptools can't find pyqt5. Maybe because the dist-info folder is missing? + postPatch = '' + substituteInPlace setup.py --replace 'pyqt5;python_version>="3"' ' ' + ''; + propagatedBuildInputs = [ - jedi pycodestyle psutil qtpy pyflakes rope numpy scipy matplotlib pylint - numpydoc qtconsole qtawesome nbconvert mccabe + jedi pycodestyle psutil pyflakes rope numpy scipy matplotlib pylint + numpydoc qtconsole qtawesome nbconvert mccabe pyopengl cloudpickle ]; # There is no test for spyder |