diff options
Diffstat (limited to 'pkgs/applications/science')
6 files changed, 312 insertions, 10 deletions
diff --git a/pkgs/applications/science/biology/blast/default.nix b/pkgs/applications/science/biology/blast/default.nix new file mode 100644 index 00000000000..ad737c6699d --- /dev/null +++ b/pkgs/applications/science/biology/blast/default.nix @@ -0,0 +1,108 @@ +{ lib, stdenv, fetchurl, zlib, bzip2, perl, cpio, gawk, coreutils, ApplicationServices }: + +stdenv.mkDerivation rec { + pname = "blast"; + version = "2.10.0"; + + src = fetchurl { + url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz"; + sha256 = "09nry5knj5hhxpn0a5ww1gb1704grd4r1y7adbjl6kqwq37dkk9s"; + }; + + sourceRoot = "ncbi-blast-${version}+-src/c++"; + + configureFlags = [ + # With flat Makefile we can use all_projects in order not to build extra. + # These extra cause clang to hang on Darwin. + "--with-flat-makefile" + "--without-makefile-auto-update" + "--with-dll" # build dynamic libraries (static are default) + ]; + + makeFlags = [ "all_projects=app/" ]; + + preConfigure = '' + export NCBICXX_RECONF_POLICY=warn + export PWD=$(pwd) + export HOME=$PWD + + # The configure scripts wants to set AR="ar cr" unless it is already set in + # the environment. Because stdenv sets AR="ar", the result is a bad call to + # the assembler later in the process. Thus, we need to unset AR + unset AR + + for awks in scripts/common/impl/is_log_interesting.awk \ + scripts/common/impl/report_duplicates.awk; do + + substituteInPlace $awks \ + --replace /usr/bin/awk ${gawk}/bin/awk + done + + for mk in src/build-system/Makefile.meta.in \ + src/build-system/helpers/run_with_lock.c ; do + + substituteInPlace $mk \ + --replace /bin/rm ${coreutils}/bin/rm + done + + for mk in src/build-system/Makefile.meta.gmake=no \ + src/build-system/Makefile.meta_l \ + src/build-system/Makefile.meta_r \ + src/build-system/Makefile.requirements \ + src/build-system/Makefile.rules_with_autodep.in; do + + substituteInPlace $mk \ + --replace /bin/echo ${coreutils}/bin/echo + done + for mk in src/build-system/Makefile.meta_p \ + src/build-system/Makefile.rules_with_autodep.in \ + src/build-system/Makefile.protobuf.in ; do + + substituteInPlace $mk \ + --replace /bin/mv ${coreutils}/bin/mv + done + + + substituteInPlace src/build-system/configure \ + --replace /bin/pwd ${coreutils}/bin/pwd \ + --replace /bin/ln ${coreutils}/bin/ln + + substituteInPlace src/build-system/configure.ac \ + --replace /bin/pwd ${coreutils}/bin/pwd \ + --replace /bin/ln ${coreutils}/bin/ln + + substituteInPlace src/build-system/Makefile.meta_l \ + --replace /bin/date ${coreutils}/bin/date + ''; + + nativeBuildInputs = [ perl ]; + + # perl is necessary in buildInputs so that installed perl scripts get patched + # correctly + buildInputs = [ coreutils perl gawk zlib bzip2 cpio ] + ++ lib.optionals stdenv.isDarwin [ ApplicationServices ]; + hardeningDisable = [ "format" ]; + + postInstall = '' + substituteInPlace $out/bin/get_species_taxids.sh \ + --replace /bin/rm ${coreutils}/bin/rm + ''; + patches = [ ./no_slash_bin.patch ]; + + enableParallelBuilding = true; + + # Many tests require either network access or locally available databases + doCheck = false; + + meta = with stdenv.lib; { + description = ''Basic Local Alignment Search Tool (BLAST) finds regions of + similarity between biological sequences''; + homepage = https://blast.ncbi.nlm.nih.gov/Blast.cgi; + license = licenses.publicDomain; + + # Version 2.10.0 fails on Darwin + # See https://github.com/NixOS/nixpkgs/pull/61430 + platforms = platforms.linux; + maintainers = with maintainers; [ luispedro ]; + }; +} diff --git a/pkgs/applications/science/biology/blast/no_slash_bin.patch b/pkgs/applications/science/biology/blast/no_slash_bin.patch new file mode 100644 index 00000000000..9b78ac57926 --- /dev/null +++ b/pkgs/applications/science/biology/blast/no_slash_bin.patch @@ -0,0 +1,184 @@ +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh 2014-08-01 22:01:17.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh 2019-05-15 12:40:44.145239480 +0800 +@@ -1,8 +1,5 @@ + #!/bin/sh + set -e +-PATH=/bin:/usr/bin +-export PATH +-unset CDPATH + + base=$1 + search=`echo ${2-$LD_LIBRARY_PATH} | tr : ' '` +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh 2011-08-17 02:55:10.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh 2019-05-15 12:40:48.449276574 +0800 +@@ -1,9 +1,6 @@ + #!/bin/sh + id='$Id: create_flat_tuneups.sh 331412 2011-08-16 18:55:10Z ucko $' + +-PATH=/bin:/usr/bin +-export PATH +- + exec > auto_flat_tuneups.mk + + cat <<EOF +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh 2011-08-20 04:12:28.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh 2019-05-15 12:40:52.901315000 +0800 +@@ -1,7 +1,5 @@ + #!/bin/sh + +-PATH=/bin:/usr/bin +-export PATH + + dir=$1.lock + +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh 2014-07-30 22:06:45.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh 2019-05-15 12:42:57.298410841 +0800 +@@ -4,9 +4,6 @@ + # Author: Denis Vakatov (vakatov@ncbi.nlm.nih.gov) + ################################# + +-orig_PATH=$PATH +-PATH=/bin:/usr/bin +- + script_name=`basename $0` + script_args="$*" + +@@ -16,7 +13,7 @@ + base_action=`basename "$action"` + case "$base_action" in + cp | cp\ * | ln | ln\ * ) +- action=/bin/$base_action ++ action=$base_action + rm="rm -f" + ;; + * ) +@@ -58,10 +55,8 @@ + shift + cmd="$* $dest_file" + test "$quiet" = yes || echo "$cmd" +- PATH=$orig_PATH + "$@" "$dest" + status=$? +- PATH=/bin:/usr/bin + return $status + } + +@@ -74,7 +69,7 @@ + case "$base_action" in + ln | ln\ -f ) + test "$quiet" = yes || echo "failed; trying \"cp -p ...\" instead" +- cmd="/bin/cp -p $src_file $dest_file" ++ cmd="cp -p $src_file $dest_file" + ExecHelper "$dest_file" /bin/cp -p "$src_file" || + Usage "\"$cmd\" failed" + ;; +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh 2011-11-17 04:43:52.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh 2019-05-15 12:40:56.769348434 +0800 +@@ -1,8 +1,6 @@ + #!/bin/sh + # $Id: make_lock_map.sh 344587 2011-11-16 20:43:52Z ucko $ + +-PATH=/bin:/usr/bin +-export PATH + + act=false + cache_dir='.#SRC-cache' +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh 2015-10-29 22:36:05.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh 2019-05-15 12:41:53.401842849 +0800 +@@ -1,10 +1,6 @@ + #!/bin/sh + # $Id: run_with_lock.sh 483249 2015-10-29 14:36:05Z ucko $ + +-orig_PATH=$PATH +-PATH=/bin:/usr/bin +-export PATH +- + base= + logfile= + map= +@@ -23,7 +19,7 @@ + : ${base:=`basename "$1"`} + + clean_up () { +- /bin/rm -rf "$base.lock" ++ rm -rf "$base.lock" + } + + case $0 in +@@ -45,7 +41,7 @@ + trap "clean_up; exit $error_status" 1 2 15 + if [ -n "$logfile" ]; then + status_file=$base.lock/status +- (PATH=$orig_PATH; export PATH; "$@"; echo $? > "$status_file") 2>&1 \ ++ ("$@"; echo $? > "$status_file") 2>&1 \ + | tee "$logfile.new" + # Emulate egrep -q to avoid having to move from under scripts. + if [ ! -f "$logfile" ] \ +@@ -58,8 +54,6 @@ + status=1 + fi + else +- PATH=$orig_PATH +- export PATH + "$@" + status=$? + fi +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh 2013-09-24 03:06:51.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh 2019-05-15 12:40:13.272975092 +0800 +@@ -1,8 +1,5 @@ + #!/bin/sh + +-PATH=/bin:/usr/bin:/usr/ccs/bin +-export PATH +- + case "$1" in + --dirs ) + shift +--- ncbi-blast-2.9.0+-src/scripts/common/impl/update_configurable.sh 2017-07-13 22:53:24.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/update_configurable.sh 2019-05-15 15:03:35.861276083 +0800 +@@ -1,6 +1,4 @@ + #!/bin/sh +-PATH=/bin:/usr/bin +-export PATH + + script_name=`basename $0` + script_dir=`dirname $0` +--- ncbi-blast-2.9.0+-src/src/build-system/Makefile.mk.in 2019-01-04 01:38:37.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/src/build-system/Makefile.mk.in 2019-05-15 15:14:41.749416495 +0800 +@@ -50,12 +50,12 @@ + + ### Auxiliary commands, filters + +-RM = /bin/rm -f +-RMDIR = /bin/rm -rf +-COPY = /bin/cp -p ++RM = rm -f ++RMDIR = rm -rf ++COPY = cp -p + BINCOPY = @BINCOPY@ + TOUCH = @TOUCH@ +-MKDIR = /bin/mkdir ++MKDIR = mkdir + BINTOUCH = $(TOUCH) + LN_S = @LN_S@ + GREP = @GREP@ +--- ncbi-blast-2.9.0+-src/src/build-system/configure 2019-03-05 00:49:08.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure 2019-05-15 16:55:40.711795042 +0800 +@@ -10417,10 +10417,6 @@ + echo "${ECHO_T}no, using $LN_S" >&6; } + fi + +-case "$LN_S" in +- /*) ;; +- * ) LN_S=/bin/$LN_S ;; +-esac + + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 5ece9a463d4..c9e546dc2ce 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1042"; + version = "1045"; src = fetchurl { url = "http://last.cbrc.jp/last-${version}.zip"; - sha256 = "0mgbhd01m9riqza2gx56qk6x5682kg71zflhisr6d3q05wrv103f"; + sha256 = "0x2wrm52ca935n3yc486m8yy59ap34w1x9h3csjca3jab5agnjkc"; }; nativeBuildInputs = [ unzip ]; diff --git a/pkgs/applications/science/chemistry/openmolcas/default.nix b/pkgs/applications/science/chemistry/openmolcas/default.nix index 487558a23c1..d73e86d2f57 100644 --- a/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchFromGitLab, cmake, gfortran, perl , openblas, hdf5-cpp, python3, texlive , armadillo, openmpi, globalarrays, openssh -, makeWrapper +, makeWrapper, fetchpatch } : let - version = "18.09"; + version = "19.11"; gitLabRev = "v${version}"; python = python3.withPackages (ps : with ps; [ six pyparsing ]); @@ -18,9 +18,19 @@ in stdenv.mkDerivation { owner = "Molcas"; repo = "OpenMolcas"; rev = gitLabRev; - sha256 = "1di1ygifx7ycfpwh25mv76xlv15wqfdmqzjsg5nani2d5z0arri2"; + sha256 = "1wwqhkyyi7pw5x1ghnp83ir17zl5jsj7phhqxapybyi3bmg0i00q"; }; + patches = [ (fetchpatch { + name = "Fix-MPI-INT-size"; # upstream patch, fixes a Fortran compiler error + url = "https://gitlab.com/Molcas/OpenMolcas/commit/860e3350523f05ab18e49a428febac8a4297b6e4.patch"; + sha256 = "0h96h5ikbi5l6ky41nkxmxfhjiykkiifq7vc2s3fdy1r1siv09sb"; + }) (fetchpatch { + name = "fix-cisandbox"; # upstream patch, fixes a Fortran compiler error + url = "https://gitlab.com/Molcas/OpenMolcas/commit/d871590c8ce4689cd94cdbbc618954c65589393d.patch"; + sha256 = "0dgz1w2rkglnis76spai3m51qa72j4bz6ppnk5zmzrr6ql7gwpgg"; + })]; + nativeBuildInputs = [ perl cmake texlive.combined.scheme-minimal makeWrapper ]; buildInputs = [ gfortran diff --git a/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix index 75c49591675..a08c0ee3403 100644 --- a/pkgs/applications/science/math/geogebra/default.nix +++ b/pkgs/applications/science/math/geogebra/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "geogebra"; - version = "5-0-569-0"; + version = "5-0-570-0"; preferLocalBuild = true; @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { "https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2" "http://web.archive.org/https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2" ]; - sha256 = "16bav6hf80l21gnhdjll82hpjqi7kr3w74jcq7mnf24acmcn70qm"; + sha256 = "0q6brg5rkl2gyyg9vhiilvb8zy23zlp4a1xcwnv501xzcccv0p37"; }; srcIcon = fetchurl { diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index 4dc6f038ce7..7536d071f6b 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -9,11 +9,11 @@ }: stdenv.mkDerivation { - name = "gromacs-2019.4"; + name = "gromacs-2020"; src = fetchurl { - url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.4.tar.gz"; - sha256 = "0rqqrbjrdhprlw2z6cqid59xwxfdx05ikvywppvdp8f8vzp6chxs"; + url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz"; + sha256 = "00ds83n5wnm7g7wq91jycp8h82vnam5b4rwg3fv9rk9x5ca5czj7"; }; nativeBuildInputs = [ cmake ]; |