diff options
Diffstat (limited to 'pkgs/applications/science')
14 files changed, 99 insertions, 67 deletions
diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index 5e899568a7df..1ad1647c70e5 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -1,18 +1,16 @@ -{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, bash }: +{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, python, bash }: stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "bcftools"; - version = "1.7"; + version = "1.8"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2"; - sha256 = "1l82sgw86l1626b7kxv3h0696lbj7317bb48rvqb1zqd3gcn6kyx"; + sha256 = "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"; }; - nativeBuildInputs = [ perl ]; - - buildInputs = [ htslib zlib bzip2 lzma curl ]; + buildInputs = [ htslib zlib bzip2 lzma curl perl python ]; makeFlags = [ "HSTDIR=${htslib}" diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 853203e7dbb1..bf963958406d 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "igv-${version}"; - version = "2.4.9"; + version = "2.4.10"; src = fetchurl { url = "http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip"; - sha256 = "0acyq7602g2pz6mc9ip1297c68kgl9pq9yzk3k2lli9l5qvxi3g1"; + sha256 = "1wyv3ny06m6ipb83hi3pzcc50v49zms69c5714iixh0nqpd826f2"; }; buildInputs = [ unzip jre ]; diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index ddcfbf00bf9e..3fc84228efe9 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "picard-tools-${version}"; - version = "2.17.11"; + version = "2.18.1"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "1p50bzkwq5hrwal6i679yrkdqkh5hk4bb9l9gdff2x2i761v9y9b"; + sha256 = "0wcihlgaif79r0fa47kq77igxzq0lpyn74414v9n6k9rl5nj8x1a"; }; buildInputs = [ jre makeWrapper ]; diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index 4da7f0f608f7..671c53365aba 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "gtkwave-${version}"; - version = "3.3.87"; + version = "3.3.89"; src = fetchurl { url = "mirror://sourceforge/gtkwave/${name}.tar.gz"; - sha256 = "0yjvxvqdl276wv0y55bqxwna6lwc99hy6dkfiy6bij3nd1qm5rf6"; + sha256 = "1j7byy0kmapa66dp17gjvs4pa4gckjccljydixswdknpxs5ma45g"; }; nativeBuildInputs = [ pkgconfig ]; diff --git a/pkgs/applications/science/logic/abella/default.nix b/pkgs/applications/science/logic/abella/default.nix index 968404362fcd..7d71a56fa23e 100644 --- a/pkgs/applications/science/logic/abella/default.nix +++ b/pkgs/applications/science/logic/abella/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "abella-${version}"; - version = "2.0.4"; + version = "2.0.5"; src = fetchurl { url = "http://abella-prover.org/distributions/${name}.tar.gz"; - sha256 = "1hnccjlyzwgz7kqsr4xmx9y4wmalbxsj0g6fxdk6xrgpc84ihw2c"; + sha256 = "0bry4pj6p9y7sg79ygdksynml4rdsjhqi959vnnwwsbaysa3bci0"; }; buildInputs = [ rsync ] ++ (with ocamlPackages; [ ocaml ocamlbuild findlib ]); diff --git a/pkgs/applications/science/logic/beluga/default.nix b/pkgs/applications/science/logic/beluga/default.nix new file mode 100644 index 000000000000..da0e9bf1c1dd --- /dev/null +++ b/pkgs/applications/science/logic/beluga/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, ocamlPackages, omake }: + +stdenv.mkDerivation { + name = "beluga-20180403"; + + src = fetchFromGitHub { + owner = "Beluga-lang"; + repo = "Beluga"; + rev = "046aa59f008be70a7c4700b723bed0214ea8b687"; + sha256 = "0m68y0r0wdw3mg2jks68bihaww7sg305zdfnic1rkndq2cxv0mld"; + }; + + nativeBuildInputs = with ocamlPackages; [ findlib ocamlbuild omake ]; + buildInputs = with ocamlPackages; [ ocaml ulex ocaml_extlib ]; + + installPhase = '' + mkdir -p $out + cp -r bin $out/ + + mkdir -p $out/share/beluga + cp -r tools/ examples/ $out/share/beluga + + mkdir -p $out/share/emacs/site-lisp/beluga/ + cp -r tools/beluga-mode.el $out/share/emacs/site-lisp/beluga + ''; + + meta = { + description = "A functional language for reasoning about formal systems"; + homepage = http://complogic.cs.mcgill.ca/beluga/; + license = stdenv.lib.licenses.gpl3Plus; + maintainers = [ stdenv.lib.maintainers.bcdarwin ]; + platforms = stdenv.lib.platforms.unix; + }; +} diff --git a/pkgs/applications/science/logic/tamarin-prover/default.nix b/pkgs/applications/science/logic/tamarin-prover/default.nix index 796b36c91735..7a9dcc231929 100644 --- a/pkgs/applications/science/logic/tamarin-prover/default.nix +++ b/pkgs/applications/science/logic/tamarin-prover/default.nix @@ -70,6 +70,9 @@ mkDerivation (common "tamarin-prover" src // { postInstall = '' wrapProgram $out/bin/tamarin-prover \ --prefix PATH : ${lib.makeBinPath [ which maude graphviz sapic ]} + # so that the package can be used as a vim plugin to install syntax coloration + install -Dt $out/share/vim-plugins/tamarin-prover/syntax/ etc/{spthy,sapic}.vim + install etc/filetype.vim -D $out/share/vim-plugins/tamarin-prover/ftdetect/tamarin.vim ''; checkPhase = "./dist/build/tamarin-prover/tamarin-prover test"; diff --git a/pkgs/applications/science/logic/workcraft/default.nix b/pkgs/applications/science/logic/workcraft/default.nix new file mode 100644 index 000000000000..9ae5d75c4577 --- /dev/null +++ b/pkgs/applications/science/logic/workcraft/default.nix @@ -0,0 +1,33 @@ +{ stdenv, pkgs, fetchurl, jre, makeWrapper }: + +stdenv.mkDerivation rec { + name = "workcraft-${version}"; + version = "3.1.9"; + + src = fetchurl { + url = "https://github.com/workcraft/workcraft/releases/download/v${version}/workcraft-v${version}-linux.tar.gz"; + sha256 = "0d1mi8jffwr7irp215j9rfpa3nmwxrx6mv13bh7vn0qf6i0aw0xi"; + }; + + buildInputs = [ makeWrapper ]; + + phases = [ "unpackPhase" "installPhase" "fixupPhase" ]; + + installPhase = '' + mkdir -p $out/share + cp -r * $out/share + mkdir $out/bin + makeWrapper $out/share/workcraft $out/bin/workcraft \ + --set JAVA_HOME "${jre}" \ + --set _JAVA_OPTIONS '-Dawt.useSystemAAFontSettings=gasp'; + ''; + + meta = { + homepage = http://workcraft.org/; + description = "Framework for interpreted graph modeling, verification and synthesis"; + platforms = stdenv.lib.platforms.linux; + license = stdenv.lib.licenses.mit; + maintainers = with stdenv.lib.maintainers; [ timor ]; + inherit version; + }; +} diff --git a/pkgs/applications/science/logic/z3/4.5.0.nix b/pkgs/applications/science/logic/z3/4.5.0.nix deleted file mode 100644 index 827cb2cbe3de..000000000000 --- a/pkgs/applications/science/logic/z3/4.5.0.nix +++ /dev/null @@ -1,31 +0,0 @@ -{ stdenv, fetchFromGitHub, python2, fixDarwinDylibNames }: - -let - python = python2; -in stdenv.mkDerivation rec { - name = "z3-${version}"; - version = "4.5.0"; - - src = fetchFromGitHub { - owner = "Z3Prover"; - repo = "z3"; - rev = "z3-4.5.0"; - sha256 = "0ssp190ksak93hiz61z90x6hy9hcw1ywp8b2dzmbhn6fbd4bnxzp"; - }; - - buildInputs = [ python fixDarwinDylibNames ]; - enableParallelBuilding = true; - - configurePhase = '' - ${python.interpreter} scripts/mk_make.py --prefix=$out --python --pypkgdir=$out/${python.sitePackages} - cd build - ''; - - meta = { - description = "A high-performance theorem prover and SMT solver"; - homepage = "https://github.com/Z3Prover/z3"; - license = stdenv.lib.licenses.mit; - platforms = stdenv.lib.platforms.unix; - maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; - }; -} diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix index e29ff24e250f..6acaa4067440 100644 --- a/pkgs/applications/science/math/giac/default.nix +++ b/pkgs/applications/science/math/giac/default.nix @@ -9,11 +9,11 @@ assert enableGUI -> libGLU_combined != null && xorg != null && fltk != null; stdenv.mkDerivation rec { name = "${attr}-${version}"; attr = if enableGUI then "giac-with-xcas" else "giac"; - version = "1.4.9"; + version = "1.4.9-59"; src = fetchurl { - url = "https://www-fourier.ujf-grenoble.fr/~parisse/giac/giac-${version}.tar.bz2"; - sha256 = "1n7xxgpqrsq7cv5wgcmgag6jvxw5wijkf1yv1r5aizlf1rc7dhai"; + url = "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version}.tar.gz"; + sha256 = "0dv5p5y6gkrsmz3xa7fw87rjyabwdwk09mqb09kb7gai9n9dgayk"; }; postPatch = '' diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index b02a65532577..ce3f975b85b8 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "qalculate-gtk-${version}"; - version = "2.2.1"; + version = "2.3.0"; src = fetchurl { url = "https://github.com/Qalculate/qalculate-gtk/archive/v${version}.tar.gz"; - sha256 = "0sf4ywz8hsszaf0yr0ncdlp7mwjk6b276bwl0j9vf1j925c89pbn"; + sha256 = "0j5wp6bmnwkyxlvqci6ddg478a0ms93gicvycw0c6bkvs2gd77az"; }; patchPhase = '' diff --git a/pkgs/applications/science/math/weka/default.nix b/pkgs/applications/science/math/weka/default.nix index 6a692e07c433..3bfb22dad936 100644 --- a/pkgs/applications/science/math/weka/default.nix +++ b/pkgs/applications/science/math/weka/default.nix @@ -1,28 +1,24 @@ -{ stdenv, fetchurl, jre, unzip }: +{ stdenv, fetchurl, jre, unzip, makeWrapper }: stdenv.mkDerivation rec { name = "weka-${version}"; - version = "3.8.2"; + version = "3.9.2"; src = fetchurl { url = "mirror://sourceforge/weka/${stdenv.lib.replaceChars ["."]["-"] name}.zip"; - sha256 = "0p353lhhcv3swwn1bl64vkyjk480vv9ghhlyqjxiar4p3xifjayb"; + sha256 = "0zwmhspmqb0a7cm6k6i0s6q3w19ws1g9dx3cp2v3g3vsif6cdh31"; }; - buildInputs = [ unzip ]; + buildInputs = [ unzip makeWrapper ]; # The -Xmx1000M comes suggested from their download page: # http://www.cs.waikato.ac.nz/ml/weka/downloading.html installPhase = '' - mkdir -pv $out/share/weka $out/bin + mkdir -pv $out/share/weka cp -Rv * $out/share/weka - cat > $out/bin/weka << EOF - #!${stdenv.shell} - ${jre}/bin/java -Xmx1000M -jar $out/share/weka/weka.jar - EOF - - chmod +x $out/bin/weka + makeWrapper ${jre}/bin/java $out/bin/weka \ + --add-flags "-Xmx1000M -jar $out/share/weka/weka.jar" ''; meta = { diff --git a/pkgs/applications/science/misc/openmvs/default.nix b/pkgs/applications/science/misc/openmvs/default.nix index 177f8ca25649..ef539ac9c8df 100644 --- a/pkgs/applications/science/misc/openmvs/default.nix +++ b/pkgs/applications/science/misc/openmvs/default.nix @@ -3,14 +3,13 @@ , gmp, mpfr, glog, google-gflags, libjpeg_turbo }: stdenv.mkDerivation rec { - name = "openmvs-unstable-2017-05-01"; + name = "openmvs-unstable-2018-05-26"; src = fetchFromGitHub { owner = "cdcseacave"; repo = "openmvs"; - - rev = "a3b360016660a1397f6eb6c070c2c19bbb4c7590"; - sha256 = "170ff4ipix2kqq5rhb1yrrcvc79im9qgp5hiwsdr23xxzdl21221"; + rev = "939033c55b50478339084431aac2c2318041afad"; + sha256 = "12dgkwwfdp24581y3i41gsd1k9hq0aw917q0ja5s0if4qbmc8pni"; }; buildInputs = [ eigen opencv ceres-solver cgal boost vcg gmp mpfr glog google-gflags libjpeg_turbo ]; diff --git a/pkgs/applications/science/spyder/default.nix b/pkgs/applications/science/spyder/default.nix index ed6e6334a5d7..4b3ef167d532 100644 --- a/pkgs/applications/science/spyder/default.nix +++ b/pkgs/applications/science/spyder/default.nix @@ -10,11 +10,11 @@ buildPythonApplication rec { pname = "spyder"; - version = "3.2.7"; + version = "3.2.8"; src = fetchPypi { inherit pname version; - sha256 = "b5bb8fe0a556930dc09b68fa2741a0de3da6488843ec960e0c62f1f3b2e08e2f"; + sha256 = "0iwcby2bxvayz0kp282yh864br55w6gpd8rqcdj1cp3jbn3q6vg5"; }; # Somehow setuptools can't find pyqt5. Maybe because the dist-info folder is missing? |