diff options
Diffstat (limited to 'pkgs/applications/science')
8 files changed, 79 insertions, 89 deletions
diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 0d8d87ac4109b..ba0114c7b5633 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 = "2.17.3"; + version = "2.17.4"; src = fetchzip { url = "https://data.broadinstitute.org/igv/projects/downloads/${lib.versions.majorMinor version}/IGV_${version}.zip"; - sha256 = "sha256-SGqkWBv4nol0+lnGN7wBHJvndcIqZ5+Wt1wAcXA42cU="; + sha256 = "sha256-LF/rwm/XlLHAJjiAlQVTmx5l+5Np2b5rPjoCdN/qERU="; }; installPhase = '' diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 3bc84e414bb75..85fb1ca80ac65 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1542"; + version = "1543"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-ZzvyyecYiBscogfN9/FnDbHg/lqb8y14n9C2KLIqhFA="; + hash = "sha256-APHPv7Q64JITfHsvjCThZ6hvGHerk6wjOm32KdTv4k8="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index 7b7b54201bf7d..584f59ba8b472 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -16,11 +16,11 @@ stdenv.mkDerivation rec { pname = "gtkwave"; - version = "3.3.118"; + version = "3.3.119"; src = fetchurl { url = "mirror://sourceforge/gtkwave/${pname}-gtk3-${version}.tar.gz"; - sha256 = "sha256-D0MwwCiiqz0vTUzur222kl2wEMS2/VLRECLQ5d6gSGo="; + sha256 = "sha256-6rPgnnZBEVwHhIv7MPfdDDu+K4y+RQF+leB327pqwDg="; }; nativeBuildInputs = [ pkg-config wrapGAppsHook ]; diff --git a/pkgs/applications/science/math/scotch/default.nix b/pkgs/applications/science/math/scotch/default.nix deleted file mode 100644 index 1eb057cfc7c5c..0000000000000 --- a/pkgs/applications/science/math/scotch/default.nix +++ /dev/null @@ -1,36 +0,0 @@ -{ lib, stdenv, fetchurl, bison, mpi, flex, zlib}: - -stdenv.mkDerivation rec { - version = "6.1.1"; - pname = "scotch"; - src_name = "scotch_${version}"; - - buildInputs = [ bison mpi flex zlib ]; - - src = fetchurl { - url = "https://gforge.inria.fr/frs/download.php/file/34618/${src_name}.tar.gz"; - sha256 = "sha256-OQUvWf9HSkppzvwlzzyvhClACIneugEO5kA8oYj4sxE="; - }; - - sourceRoot = "${src_name}/src"; - - preConfigure = '' - ln -s Make.inc/Makefile.inc.x86-64_pc_linux2 Makefile.inc - ''; - - buildFlags = [ "scotch ptscotch" ]; - installFlags = [ "prefix=\${out}" ]; - - meta = { - description = "Graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering"; - longDescription = '' - Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, - and sparse matrix ordering. - ''; - homepage = "http://www.labri.fr/perso/pelegrin/scotch"; - license = lib.licenses.cecill-c; - maintainers = [ lib.maintainers.bzizou ]; - platforms = lib.platforms.linux; - }; -} - diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index 9548db1c7c479..59bb9415b37d9 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -53,12 +53,11 @@ , Cocoa , CoreSymbolication , OpenGL -, noSplash ? false }: stdenv.mkDerivation rec { pname = "root"; - version = "6.30.04"; + version = "6.30.06"; passthru = { tests = import ./tests { inherit callPackage; }; @@ -66,7 +65,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://root.cern.ch/download/root_v${version}.source.tar.gz"; - hash = "sha256-K0GAtpjznMZdkQhNgzqIRRWzJbxfZzyOOavoGLAl2Mw="; + hash = "sha256-MA237RtnjtL7ljXKZ1khoZRcfCED2oQAM7STCR9VcAw="; }; nativeBuildInputs = [ makeWrapper cmake pkg-config git ]; @@ -143,8 +142,6 @@ stdenv.mkDerivation rec { -e '1iset(nlohmann_json_DIR "${nlohmann_json}/lib/cmake/nlohmann_json/")' patchShebangs build/unix/ - '' + lib.optionalString noSplash '' - substituteInPlace rootx/src/rootx.cxx --replace "gNoLogo = false" "gNoLogo = true" '' + lib.optionalString stdenv.isDarwin '' # Eliminate impure reference to /System/Library/PrivateFrameworks substituteInPlace core/macosx/CMakeLists.txt \ @@ -163,10 +160,6 @@ stdenv.mkDerivation rec { "-Dbuiltin_gtest=OFF" "-Dbuiltin_nlohmannjson=OFF" "-Dbuiltin_openui5=ON" - "-Dalien=OFF" - "-Dbonjour=OFF" - "-Dcastor=OFF" - "-Dchirp=OFF" "-Dclad=OFF" "-Ddavix=ON" "-Ddcache=OFF" @@ -176,21 +169,13 @@ stdenv.mkDerivation rec { "-Dfortran=OFF" "-Dgnuinstall=ON" "-Dimt=ON" - "-Dgfal=OFF" "-Dgviz=OFF" - "-Dhdfs=OFF" "-Dhttp=ON" - "-Dkrb5=OFF" - "-Dldap=OFF" - "-Dmonalisa=OFF" "-Dmysql=OFF" "-Dodbc=OFF" "-Dopengl=ON" - "-Doracle=OFF" "-Dpgsql=OFF" - "-Dpythia6=OFF" "-Dpythia8=OFF" - "-Drfio=OFF" "-Droot7=ON" "-Dsqlite=OFF" "-Dssl=ON" @@ -204,16 +189,12 @@ stdenv.mkDerivation rec { ++ lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${lib.getDev stdenv.cc.libc}/include" ++ lib.optionals stdenv.isDarwin [ "-DOPENGL_INCLUDE_DIR=${OpenGL}/Library/Frameworks" - "-DCMAKE_DISABLE_FIND_PACKAGE_Python2=TRUE" # fatal error: module map file '/nix/store/<hash>-Libsystem-osx-10.12.6/include/module.modulemap' not found # fatal error: could not build module '_Builtin_intrinsics' "-Druntime_cxxmodules=OFF" ]; - # suppress warnings from compilation of the vendored clang to avoid running into log limits on the Hydra - NIX_CFLAGS_COMPILE = lib.optionals stdenv.cc.isGNU [ "-Wno-shadow" "-Wno-maybe-uninitialized" ]; - postInstall = '' for prog in rootbrowse rootcp rooteventselector rootls rootmkdir rootmv rootprint rootrm rootslimtree; do wrapProgram "$out/bin/$prog" \ @@ -273,7 +254,7 @@ stdenv.mkDerivation rec { homepage = "https://root.cern.ch/"; description = "A data analysis framework"; platforms = platforms.unix; - maintainers = [ maintainers.veprbl ]; + maintainers = [ maintainers.guitargeek maintainers.veprbl ]; license = licenses.lgpl21; }; } diff --git a/pkgs/applications/science/physics/crystfel/default.nix b/pkgs/applications/science/physics/crystfel/default.nix index 92b48ec863091..33f2043603177 100644 --- a/pkgs/applications/science/physics/crystfel/default.nix +++ b/pkgs/applications/science/physics/crystfel/default.nix @@ -6,15 +6,16 @@ , fetchzip , cmake , lz4 +, gfortran , bzip2 -, m4 , hdf5 , gsl , unzip , makeWrapper +, zlib , meson -, git , ninja +, pandoc , eigen , pkg-config , wrapGAppsHook @@ -40,7 +41,7 @@ let pname = "libccp4"; version = "8.0.0"; src = fetchurl { - url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz"; + url = "https://ftp.ccp4.ac.uk/opensource/libccp4-${version}.tar.gz"; hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0="; }; nativeBuildInputs = [ meson ninja ]; @@ -87,7 +88,7 @@ let }; mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11"; in - stdenv.mkDerivation rec { + stdenv.mkDerivation { pname = "mosflm"; inherit version src; @@ -111,7 +112,7 @@ let pname = "xgandalf"; version = "c6c5003ff1086e8c0fb5313660b4f02f3a3aab7b"; src = fetchurl { - url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz"; + url = "https://gitlab.desy.de/thomas.white/xgandalf/-/archive/${version}/xgandalf-${version}.tar.gz"; hash = "sha256-/uZlBwAINSoYqgLQFTMz8rS1Rpadu79JkO6Bu/+Nx9E="; }; @@ -121,10 +122,10 @@ let pinkIndexer = stdenv.mkDerivation rec { pname = "pinkindexer"; - version = "5d4e016941eb2a9e50a10df96ded7ff1e2464503"; + version = "15caa21191e27e989b750b29566e4379bc5cd21a"; src = fetchurl { url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz"; - hash = "sha256-VnJOJJ247dNoBlos4Fu3GQBlAnTk9el+yZDRiicJtu0="; + hash = "sha256-v/SCJiHAV05Lc905y/dE8uBXlW+lLX9wau4XORYdbQg="; }; nativeBuildInputs = [ meson pkg-config ninja ]; @@ -169,13 +170,27 @@ let "-DENABLE_BZIP2_PLUGIN=yes" ]; }; + + millepede-ii = stdenv.mkDerivation rec { + pname = "millepede-ii"; + version = "04-13-06"; + src = fetchurl { + url = "https://gitlab.desy.de/claus.kleinwort/millepede-ii/-/archive/V${version}/millepede-ii-V${version}.tar.gz"; + hash = "sha256-aFoo8AGBsUEN2u3AmnSpTqJ6JeNV6j9vkAFTZ34I+sI="; + }; + + nativeBuildInputs = [ gfortran ]; + buildInputs = [ zlib ]; + + makeFlags = [ "PREFIX=$(out)" ]; + }; in stdenv.mkDerivation rec { pname = "crystfel"; - version = "0.10.2"; + version = "0.11.0"; src = fetchurl { - url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz"; - sha256 = "sha256-nCO9ndDKS54bVN9IhFBiCVNzqk7BsCljXFrOmlx+sP4="; + url = "https://www.desy.de/~twhite/crystfel/crystfel-${version}.tar.gz"; + sha256 = "sha256-ogNHWYfbxRmB5TdK8K0JpcCnYOOyXapQGSPh8mfp+Tc="; }; nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ] ++ lib.optionals withGui [ wrapGAppsHook ]; @@ -192,6 +207,7 @@ stdenv.mkDerivation rec { mosflm pinkIndexer xgandalf + pandoc ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ] ++ lib.optionals stdenv.isDarwin [ argp-standalone @@ -201,12 +217,12 @@ stdenv.mkDerivation rec { ++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ]; patches = [ + # on darwin at least, we need to link to a separate argp library; + # this patch adds a test for this and the necessary linker options ./link-to-argp-standalone-if-needed.patch - ./disable-fmemopen-on-aarch64-darwin.patch - (fetchpatch { - url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff"; - hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc="; - }) + # hotfix for an issue that occurs (at least) on NixOS: + # if the temporary path is too long, we get a segfault + ./gui-path-issue.patch ]; # CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but @@ -218,7 +234,9 @@ stdenv.mkDerivation rec { postInstall = lib.optionalString withBitshuffle '' for file in $out/bin/*; do - wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins + wrapProgram $file \ + --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins \ + --prefix PATH ":" ${lib.makeBinPath [ millepede-ii ]} done ''; diff --git a/pkgs/applications/science/physics/crystfel/gui-path-issue.patch b/pkgs/applications/science/physics/crystfel/gui-path-issue.patch new file mode 100644 index 0000000000000..28cd0280e8f67 --- /dev/null +++ b/pkgs/applications/science/physics/crystfel/gui-path-issue.patch @@ -0,0 +1,27 @@ +diff --git a/src/gui_index.c b/src/gui_index.c +index 2cc8e8db..13be77d5 100644 +--- a/src/gui_index.c ++++ b/src/gui_index.c +@@ -540,6 +540,7 @@ static void delete_gui_tempdir(char *tmpdir) + { + char *path; + int i; ++ size_t pathlen; + + /* List of files which it's safe to delete */ + char *files[] = {"gmon.out", "mosflm.lp", "SUMMARY", "XDS.INP", +@@ -552,11 +553,12 @@ static void delete_gui_tempdir(char *tmpdir) + + if ( tmpdir == NULL ) return; + +- path = calloc(strlen(tmpdir)+64, 1); ++ pathlen = strlen(tmpdir)+64; ++ path = calloc(pathlen, 1); + if ( path == NULL ) return; + + for ( i=0; i<n_files; i++ ) { +- snprintf(path, 127, "%s/%s", tmpdir, files[i]); ++ snprintf(path, pathlen, "%s/%s", tmpdir, files[i]); + unlink(path); + } + diff --git a/pkgs/applications/science/physics/crystfel/link-to-argp-standalone-if-needed.patch b/pkgs/applications/science/physics/crystfel/link-to-argp-standalone-if-needed.patch index 8314be29ac006..edadb750ac57f 100644 --- a/pkgs/applications/science/physics/crystfel/link-to-argp-standalone-if-needed.patch +++ b/pkgs/applications/science/physics/crystfel/link-to-argp-standalone-if-needed.patch @@ -1,8 +1,8 @@ diff --git a/meson.build b/meson.build -index 59bbcfb7..dd75d4e2 100644 +index 4717bb2a..38d8693f 100644 --- a/meson.build +++ b/meson.build -@@ -80,6 +80,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>') +@@ -70,6 +70,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>') conf_data.set10('HAVE_CLOCK_GETTIME', true) endif @@ -12,15 +12,15 @@ index 59bbcfb7..dd75d4e2 100644 + argpdep = dependency('', required : false) +endif + - # ************************ libcrystfel (subdir) ************************ - - subdir('libcrystfel') -@@ -180,7 +186,7 @@ endif + if cc.has_function('sched_setaffinity', + prefix: '#include <sched.h>', + args: '-D_GNU_SOURCE') +@@ -186,7 +192,7 @@ endif indexamajig = executable('indexamajig', indexamajig_sources, dependencies: [mdep, libcrystfeldep, gsldep, -- pthreaddep, zmqdep, asapodep], -+ pthreaddep, zmqdep, asapodep, argpdep], +- pthreaddep, zmqdep, asapodep, asapoproddep], ++ pthreaddep, zmqdep, asapodep, asapoproddep, argpdep], install: true, - install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib') + install_rpath: crystfel_rpath) |