diff options
Diffstat (limited to 'pkgs/applications/science')
18 files changed, 451 insertions, 24 deletions
diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix new file mode 100644 index 000000000000..20d88eb3aafb --- /dev/null +++ b/pkgs/applications/science/biology/EZminc/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, itk, fftwFloat, gsl }: + +stdenv.mkDerivation rec { pname = "EZminc"; + name = "${pname}-2017-08-29"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "4e017236cb6e7f6e07507446b18b759c584b6fc3"; + sha256 = "1pg06x42pgsg7zy7dz9wf6ajakkm2n8by64lg9z64qi8qqy82b8v"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ itk libminc bicpl fftwFloat gsl ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" + "-DEZMINC_BUILD_TOOLS=TRUE" + "-DEZMINC_BUILD_MRFSEG=TRUE" + "-DEZMINC_BUILD_DD=TRUE" ]; + + checkPhase = "ctest --output-on-failure ../tests/"; # but ctest doesn't find the tests ... + + enableParallelBuilding = true; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Collection of Perl and shell scripts for processing MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/pkgs/applications/science/biology/N3/default.nix b/pkgs/applications/science/biology/N3/default.nix new file mode 100644 index 000000000000..c14846beec2f --- /dev/null +++ b/pkgs/applications/science/biology/N3/default.nix @@ -0,0 +1,38 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perl, MNI-Perllib, GetoptTabular, + libminc, EBTKS }: + +stdenv.mkDerivation rec { + pname = "N3"; + name = "${pname}-2017-09-18"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "2fdd939f0f2b24a4039bc6a8ade4a190a1d8e75d"; + sha256 = "13z21c4r09hna3q1csvcn4i7ws5ixbdaja6ch421xv6nydjh2w5g"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc EBTKS ]; + propagatedBuildInputs = [ perl MNI-Perllib GetoptTabular ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + + checkPhase = "ctest --output-on-failure"; + # don't run the tests as they fail at least due to missing program wrappers in this phase ... + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB + done + ''; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "MRI non-uniformity correction for MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/pkgs/applications/science/biology/inormalize/default.nix b/pkgs/applications/science/biology/inormalize/default.nix new file mode 100644 index 000000000000..f17143ad06bb --- /dev/null +++ b/pkgs/applications/science/biology/inormalize/default.nix @@ -0,0 +1,39 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perl, GetoptTabular, MNI-Perllib, + libminc, EBTKS }: + +stdenv.mkDerivation rec { + pname = "inormalize"; + name = "${pname}-2014-10-21"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "79cea9cdfe7b99abfd40afda89ab2253b596ad2f"; + sha256 = "1ahqv5q0ljvji99a5q8azjkdf6bgp6nr8lwivkqwqs3jm0k5clq7"; + }; + + patches = [ ./lgmask-interp.patch ./nu_correct_norm-interp.patch ]; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc EBTKS ]; + propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + + checkPhase = "ctest --output-on-failure"; # but no tests + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB + done + ''; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Program to normalize intensity of MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/pkgs/applications/science/biology/inormalize/lgmask-interp.patch b/pkgs/applications/science/biology/inormalize/lgmask-interp.patch new file mode 100644 index 000000000000..953bce9a1848 --- /dev/null +++ b/pkgs/applications/science/biology/inormalize/lgmask-interp.patch @@ -0,0 +1,10 @@ +diff --git a/lgmask.in b/lgmask.in +index 17dbe4d..2195d91 100644 +--- a/lgmask.in ++++ b/lgmask.in +@@ -1,4 +1,4 @@ +-#! @PERL@ ++#! /usr/bin/env perl + + #--------------------------------------------------------------------------- + #@COPYRIGHT : diff --git a/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch b/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch new file mode 100644 index 000000000000..75dc46a799ce --- /dev/null +++ b/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch @@ -0,0 +1,10 @@ +diff --git a/nu_correct_norm.in b/nu_correct_norm.in +index 1dc84ac..1bc6235 100644 +--- a/nu_correct_norm.in ++++ b/nu_correct_norm.in +@@ -1,4 +1,4 @@ +-#! @PERL@ ++#! /usr/bin/perl + + #--------------------------------------------------------------------------- + #@COPYRIGHT : diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix index 7864658c9582..8e1f74686d1f 100644 --- a/pkgs/applications/science/biology/minc-tools/default.nix +++ b/pkgs/applications/science/biology/minc-tools/default.nix @@ -1,23 +1,29 @@ -{ stdenv, fetchFromGitHub, perl, cmake, flex, bison, libminc }: +{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perl, TextFormat, libminc, libjpeg, zlib }: stdenv.mkDerivation rec { - name = "${pname}-2.3.00"; pname = "minc-tools"; + name = "${pname}-2017-09-11"; src = fetchFromGitHub { - owner = "BIC-MNI"; - repo = pname; - rev = builtins.replaceStrings [ "." ] [ "-" ] name; - sha256 = "0px5paprx4ds9aln3jdg1pywszgyz2aykgkdbj1y8gc1lwcizsl9"; + owner = "BIC-MNI"; + repo = pname; + rev = "5b7c40425cd4f67a018055cb85c0157ee50a3056"; + sha256 = "0zkcs05svp1gj5h0cdgc0k20c7lrk8m7wg3ks3xc5mkaiannj8g7"; }; - nativeBuildInputs = [ cmake flex bison ] ++ (if doCheck then [ perl ] else [ ]); - buildInputs = [ libminc ]; + nativeBuildInputs = [ cmake flex bison makeWrapper ]; + buildInputs = [ libminc libjpeg zlib ]; + propagatedBuildInputs = [ perl TextFormat ]; cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ]; - checkPhase = "ctest"; - doCheck = false; + checkPhase = "ctest --output-on-failure"; # still some weird test failures though + + postFixup = '' + for prog in minccomplete minchistory mincpik; do + wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB + done + ''; enableParallelBuilding = true; @@ -26,5 +32,6 @@ stdenv.mkDerivation rec { description = "Command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; + license = licenses.free; }; } diff --git a/pkgs/applications/science/biology/minc-widgets/default.nix b/pkgs/applications/science/biology/minc-widgets/default.nix new file mode 100644 index 000000000000..9084dfb2e1c3 --- /dev/null +++ b/pkgs/applications/science/biology/minc-widgets/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perl, GetoptTabular, MNI-Perllib, + libminc, octave, coreutils, minc_tools }: + +stdenv.mkDerivation rec { + pname = "minc-widgets"; + name = "${pname}-2016-04-20"; + + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "f08b643894c81a1a2e0fbfe595a17a42ba8906db"; + sha256 = "1b9g6lf37wpp211ikaji4rf74rl9xcmrlyqcw1zq3z12ji9y33bm"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc ]; + propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib octave coreutils minc_tools ]; + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${stdenv.lib.makeBinPath [ coreutils minc_tools ]}"; + done + ''; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Collection of Perl and shell scripts for processing MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/pkgs/applications/science/biology/mni_autoreg/default.nix b/pkgs/applications/science/biology/mni_autoreg/default.nix new file mode 100644 index 000000000000..076ecd03a1b1 --- /dev/null +++ b/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -0,0 +1,36 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, perl, GetoptTabular, MNI-Perllib, libminc }: + +stdenv.mkDerivation rec { + pname = "mni_autoreg"; + name = "${pname}-2017-09-22"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "ab99e29987dc029737785baebf24896ec37a2d76"; + sha256 = "0axl069nv57vmb2wvqq7s9v3bfxwspzmk37bxm4973ai1irgppjq"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc ]; + propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBUILD_TESTING=FALSE" ]; + # testing broken: './minc_wrapper: Permission denied' from Testing/ellipse0.mnc + + postFixup = '' + for prog in autocrop mritoself mritotal xfmtool; do + echo $out/bin/$prog + wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB; + done + ''; + + meta = with stdenv.lib; { + homepage = https://github.com/BIC-MNI/mni_autoreg; + description = "Tools for automated registration using the MINC image format"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} + diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index 3fc84228efe9..7af1669dc45e 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "picard-tools-${version}"; - version = "2.18.1"; + version = "2.18.2"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0wcihlgaif79r0fa47kq77igxzq0lpyn74414v9n6k9rl5nj8x1a"; + sha256 = "0w3b2jz4n9irslsg85r4x9dc3y4ziykn8fs4iqqiq4sfdcz259fz"; }; buildInputs = [ jre makeWrapper ]; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix new file mode 100644 index 000000000000..c85e1143d103 --- /dev/null +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -0,0 +1,44 @@ +{ stdenv +, fetchurl +, unzip +, jre +}: + +stdenv.mkDerivation rec { + version = "${baseVersion}.${patchVersion}"; + baseVersion = "14.29"; + patchVersion = "12"; + pname = "jmol"; + name = "${pname}-${version}"; + + src = fetchurl { + url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; + sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv"; + }; + + buildInputs = [ + jre + ]; + + installPhase = '' + mkdir -p "$out/share/jmol" + mkdir -p "$out/bin" + + ${unzip}/bin/unzip jsmol.zip -d "$out/share/" + + sed -i -e 's|command=java|command=${jre}/bin/java|' jmol.sh + cp *.jar jmol.sh "$out/share/jmol" + ln -s $out/share/jmol/jmol.sh "$out/bin/jmol" + ''; + + enableParallelBuilding = true; + + meta = with stdenv.lib; { + description = "A Java 3D viewer for chemical structures"; + homepage = https://sourceforge.net/projects/jmol; + license = licenses.lgpl2; + platforms = platforms.all; + maintainers = with maintainers; [ timokau ]; + }; +} + diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix index 2ff20fef40e8..bf8ccee4a635 100644 --- a/pkgs/applications/science/chemistry/octopus/default.nix +++ b/pkgs/applications/science/chemistry/octopus/default.nix @@ -3,7 +3,7 @@ }: let - version = "7.2"; + version = "7.3"; 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 = "03zzmq72zdnjkhifbmlxs7ig7x6sf6mv8zv9mxhakm9hzwa9yn7m"; + sha256 = "0hnpqjjxdxh2ggf6ckrsy4hs9iglnazscb4siczddvmysi4kv15d"; }; nativeBuildInputs = [ perl procps fftw.dev ]; diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 2c785472114a..2b35c91d10c4 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -22,7 +22,7 @@ let "8.7.0" = "1h18b7xpnx3ix9vsi5fx4zdcbxy7bhra7gd5c5yzxmk53cgf1p9m"; "8.7.1" = "0gjn59jkbxwrihk8fx9d823wjyjh5m9gvj9l31nv6z6bcqhgdqi8"; "8.7.2" = "0a0657xby8wdq4aqb2xsxp3n7pmc2w4yxjmrb2l4kccs1aqvaj4w"; - "8.8+beta1" = "19ipmx6bf8wjpk8y29hcginxk7hps4jh1bbihn5icx4qysm81165"; + "8.8.0" = "13a4fka22hdxsjk11mgjb9ffzplfxyxp1sg5v1c8nk1grxlscgw8"; }."${version}"; coq-version = builtins.substring 0 3 version; camlp5 = ocamlPackages.camlp5_strict; @@ -34,11 +34,9 @@ let self = stdenv.mkDerivation { name = "coq-${version}"; - inherit coq-version; - inherit camlp5; - inherit (ocamlPackages) ocaml; passthru = { - inherit (ocamlPackages) findlib num; + inherit coq-version camlp5; + inherit (ocamlPackages) ocaml findlib num; emacsBufferSetup = pkgs: '' ; Propagate coq paths to children (inherit-local-permanent coq-prog-name "${self}/bin/coqtop") @@ -125,8 +123,11 @@ self = stdenv.mkDerivation { buildFlags = "revision coq coqide bin/votour"; + createFindlibDestdir = true; + postInstall = '' cp bin/votour $out/bin/ + ln -s $out/lib/coq $OCAMLFIND_DESTDIR/coq ''; meta = with stdenv.lib; { diff --git a/pkgs/applications/science/machine-learning/shogun/default.nix b/pkgs/applications/science/machine-learning/shogun/default.nix index e33b55503bd6..0ac40b1e7d42 100644 --- a/pkgs/applications/science/machine-learning/shogun/default.nix +++ b/pkgs/applications/science/machine-learning/shogun/default.nix @@ -52,6 +52,10 @@ stdenv.mkDerivation rec { ++ (optional (opencvSupport) "-DOpenCV=ON") ; + # Previous attempts to fix parallel builds (see patch above) were not entirely successful. + # Sporadic build failures still exist. Dislable parallel builds for now. + enableParallelBuilding = false; + meta = with stdenv.lib; { description = "A toolbox which offers a wide range of efficient and unified machine learning methods"; homepage = "http://shogun-toolbox.org/"; diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix index 6acaa4067440..dd92e264889f 100644 --- a/pkgs/applications/science/math/giac/default.nix +++ b/pkgs/applications/science/math/giac/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, texlive, bison, flex +{ stdenv, fetchurl, fetchpatch, texlive, bison, flex , gmp, mpfr, pari, ntl, gsl, blas, mpfi, liblapackWithAtlas , readline, gettext, libpng, libao, gfortran, perl , enableGUI ? false, libGLU_combined ? null, xorg ? null, fltk ? null @@ -16,6 +16,15 @@ stdenv.mkDerivation rec { sha256 = "0dv5p5y6gkrsmz3xa7fw87rjyabwdwk09mqb09kb7gai9n9dgayk"; }; + patches = stdenv.lib.optionals (!enableGUI) [ + # when enableGui is false, giac is compiled without fltk. That means some + # outputs differ in the make check. Patch around this: + (fetchpatch { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/nofltk-check.patch?id=7553a3c8dfa7bcec07241a07e6a4e7dcf5bb4f26"; + sha256 = "0xkmfc028vg5w6va04gp2x2iv31n8v4shd6vbyvk4blzgfmpj2cw"; + }) + ]; + postPatch = '' for i in doc/*/Makefile*; do substituteInPlace "$i" --replace "/bin/cp" "cp"; @@ -37,10 +46,11 @@ stdenv.mkDerivation rec { libGLU_combined fltk xorg.libX11 ]; - outputs = [ "out" ]; + outputs = [ "out" "doc" ]; + + doCheck = true; enableParallelBuilding = true; - hardeningDisable = [ "format" "bindnow" "relro" ]; configureFlags = [ "--enable-gc" "--enable-png" "--enable-gsl" "--enable-lapack" @@ -57,6 +67,13 @@ stdenv.mkDerivation rec { for file in $(find $out -name Makefile) ; do sed -i "s@/nix/store/[^/]*/bin/@@" "$file" ; done; + + # reference cycle + rm "$out/share/giac/doc/el/"{casinter,tutoriel}/Makefile + + mkdir -p "$doc/share/giac" + mv "$out/share/giac/doc" "$doc/share/giac" + mv "$out/share/giac/examples" "$doc/share/giac" ''; meta = with stdenv.lib; { diff --git a/pkgs/applications/science/math/lrcalc/default.nix b/pkgs/applications/science/math/lrcalc/default.nix new file mode 100644 index 000000000000..9e02b08c8ad0 --- /dev/null +++ b/pkgs/applications/science/math/lrcalc/default.nix @@ -0,0 +1,41 @@ +{ stdenv +, fetchFromBitbucket +, fetchpatch +, autoreconfHook +}: + +stdenv.mkDerivation rec { + version = "1.2"; + pname = "lrcalc"; + name = "${pname}-${version}"; + + src = fetchFromBitbucket { + owner = "asbuch"; + repo = "lrcalc"; + rev = "lrcalc-${version}"; + sha256 = "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"; + }; + + doCheck = true; + + nativeBuildInputs = [ + autoreconfHook + ]; + + patches = [ + # Fix include syntax: + # For private includes, use `#include "..."` instead of `#include <...>` + (fetchpatch { + url = "https://bitbucket.org/asbuch/lrcalc/commits/226981a0/raw/"; + sha256 = "02kaqx5s3l642rhh28kn2wg9wr098vzpknxyl4pv627lqa3lv9vm"; + }) + ]; + + meta = with stdenv.lib; { + description = "Littlewood-Richardson calculator"; + homepage = http://math.rutgers.edu/~asbuch/lrcalc/; + license = licenses.gpl2Plus; + maintainers = with maintainers; [ timokau ]; + platforms = platforms.linux; + }; +} diff --git a/pkgs/applications/science/math/palp/default.nix b/pkgs/applications/science/math/palp/default.nix new file mode 100644 index 000000000000..3484c369db3b --- /dev/null +++ b/pkgs/applications/science/math/palp/default.nix @@ -0,0 +1,67 @@ +{ stdenv +, fetchurl +, dimensions ? 6 # works for <= dimensions dimensions, but is only optimized for that exact value +, doSymlink ? true # symlink the executables to the default location (without dimension postfix) +}: + +stdenv.mkDerivation rec { + version = "2.1"; + dim = toString dimensions; + name = "palp-${dim}d-${version}"; + + src = fetchurl { + url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz"; + sha256 = "1s7s2lc5f0ig1yy7ygsh3sddm3sbq4mxwybqsj8lp9wjdxs7qfrs"; + }; + + hardeningDisable = [ "format" ]; + + preBuild = '' + echo Building PALP optimized for ${dim} dimensions + sed -i "s/^#define[^a-zA-Z]*POLY_Dmax.*/#define POLY_Dmax ${dim}/" Global.h + ''; + + installPhase = '' + mkdir -p "$out/bin" + for file in poly class cws nef mori; do + cp -p $file.x "$out/bin/$file-${dim}d.x" + done + '' + stdenv.lib.optionalString doSymlink '' + cd "$out/bin" + for file in poly class cws nef mori; do + ln -sf $file-6d.x $file.x + done + ''; + + meta = with stdenv.lib; { + description = "A Package for Analyzing Lattice Polytopes"; + longDescription = '' + A Package for Analyzing Lattice Polytopes (PALP) is a set of C + programs for calculations with lattice polytopes and applications to + toric geometry. + + It contains routines for vertex and facet enumeration, computation of + incidences and symmetries, as well as completion of the set of lattice + points in the convex hull of a given set of points. In addition, there + are procedures specialised to reflexive polytopes such as the + enumeration of reflexive subpolytopes, and applications to toric + geometry and string theory, like the computation of Hodge data and + fibration structures for toric Calabi-Yau varieties. The package is + well tested and optimised in speed as it was used for time consuming + tasks such as the classification of reflexive polyhedra in 4 + dimensions and the creation and manipulation of very large lists of + 5-dimensional polyhedra. + + While originally intended for low-dimensional applications, the + algorithms work in any dimension and our key routine for vertex and + facet enumeration compares well with existing packages. + ''; + homepage = http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html; + # Just a link on the website pointing to gpl -- now gplv3. When the last + # version was released that pointed to gplv2 however, so thats probably + # the right license. + license = licenses.gpl2; + maintainers = with maintainers; [ timokau ]; + platforms = platforms.all; + }; +} diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix new file mode 100644 index 000000000000..fd566abd9a9a --- /dev/null +++ b/pkgs/applications/science/math/pynac/default.nix @@ -0,0 +1,47 @@ +{ stdenv +, fetchFromGitHub +, autoreconfHook +, pkgconfig +, flint +, gmp +, python2 +, singular +}: + +stdenv.mkDerivation rec { + version = "0.7.19"; + name = "pynac-${version}"; + + src = fetchFromGitHub { + owner = "pynac"; + repo = "pynac"; + rev = "pynac-${version}"; + sha256 = "132bibvapm245c5xy29j3xmjs0pawvw7lv05374m8vv1m39127d3"; + }; + + buildInputs = [ + flint + gmp + singular + singular + python2 + ]; + + nativeBuildInputs = [ + autoreconfHook + pkgconfig + ]; + + meta = with stdenv.lib; { + description = "Python is Not a CAS -- modified version of Ginac"; + longDescription = '' + Pynac -- "Python is Not a CAS" is a modified version of Ginac that + replaces the depency of GiNaC on CLN by a dependency instead of Python. + It is a lite version of GiNaC as well, not implementing all the features + of the full GiNaC, and it is *only* meant to be used as a Python library. + ''; + homepage = http://pynac.org; + maintainers = with maintainers; [ timokau ]; + platforms = platforms.linux; + }; +} diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix index 0194ee0b83c0..36c7884d108b 100644 --- a/pkgs/applications/science/misc/cytoscape/default.nix +++ b/pkgs/applications/science/misc/cytoscape/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "cytoscape-${version}"; - version = "3.6.0"; + version = "3.6.1"; src = fetchurl { url = "http://chianti.ucsd.edu/${name}/${name}.tar.gz"; - sha256 = "13q8caksbzi6j7xy8v5f0pi6766yfawys6jcm50ng78mnhrv2v97"; + sha256 = "1pkdilv1nw6vvdxk71bwjngr8yafrsqwaqvlakhp8yb342r1jd4s"; }; buildInputs = [jre makeWrapper]; |