diff options
Diffstat (limited to 'pkgs/applications/science')
15 files changed, 68 insertions, 14 deletions
diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index ecca9141d9fba..59c6a02d3494f 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -6,13 +6,13 @@ mkDerivation rec { pname = "stellarium"; - version = "0.19.1"; + version = "0.19.2"; src = fetchFromGitHub { owner = "Stellarium"; repo = "stellarium"; rev = "v${version}"; - sha256 = "0hf1wv2bb5j7ny2xh29mj9m4hjblhn02zylay8gl85w7xlqs7s5r"; + sha256 = "1ki3s4smazr6xfkr0grrmjp2s8yjprismiaq7l54d0il7rkvhibd"; }; nativeBuildInputs = [ cmake perl wrapQtAppsHook ]; diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix index dbcfead6b1ea2..696162d2dc539 100644 --- a/pkgs/applications/science/biology/EZminc/default.nix +++ b/pkgs/applications/science/biology/EZminc/default.nix @@ -26,5 +26,6 @@ stdenv.mkDerivation rec { pname = "EZminc"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; license = licenses.free; + broken = true; }; } diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix new file mode 100644 index 0000000000000..bfdf5a1bb17e1 --- /dev/null +++ b/pkgs/applications/science/biology/delly/default.nix @@ -0,0 +1,40 @@ +{ stdenv, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }: + +stdenv.mkDerivation rec { + pname = "delly"; + version = "0.8.1"; + + src = fetchFromGitHub { + owner = "dellytools"; + repo = pname; + rev = "v${version}"; + sha256 = "18gm86j1g1k4z1cjv2m5v9rsl1xqs2w3dhwcsnzx2mhkrvmlc4i1"; + }; + + buildInputs = [ zlib htslib bzip2 lzma ncurses boost ]; + + EBROOTHTSLIB = htslib; + + installPhase = '' + runHook preInstall + + install -Dm555 src/delly $out/bin/delly + + runHook postInstall + ''; + + meta = with stdenv.lib; { + description = "Structural variant caller for mapped DNA sequenced data"; + license = licenses.gpl3; + maintainers = with maintainers; [ scalavision ]; + platforms = platforms.linux; + longDescription = '' + Delly is an integrated structural variant (SV) prediction method + that can discover, genotype and visualize deletions, tandem duplications, + inversions and translocations at single-nucleotide resolution in + short-read massively parallel sequencing data. It uses paired-ends, + split-reads and read-depth to sensitively and accurately delineate + genomic rearrangements throughout the genome. + ''; + }; +} diff --git a/pkgs/applications/science/biology/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix index 161188f7ef169..fe6919656d9d9 100644 --- a/pkgs/applications/science/biology/paml/default.nix +++ b/pkgs/applications/science/biology/paml/default.nix @@ -29,5 +29,6 @@ stdenv.mkDerivation rec { longDescription = ''PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.''; license = "non-commercial"; homepage = http://abacus.gene.ucl.ac.uk/software/paml.html; + broken = true; }; } diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix index 84c90d895566c..c791e8ef89bbc 100644 --- a/pkgs/applications/science/biology/strelka/default.nix +++ b/pkgs/applications/science/biology/strelka/default.nix @@ -33,6 +33,7 @@ stdenv.mkDerivation rec { homepage = https://github.com/Illumina/strelka; maintainers = with maintainers; [ jbedo ]; platforms = [ "x86_64-linux" ]; + broken = true; }; } diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 1fc387fcc66dc..b1bd01fb2f7fe 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -47,5 +47,6 @@ python3Packages.buildPythonApplication { description = description; homepage = https://www.pymol.org/; license = licenses.psfl; + broken = true; }; } diff --git a/pkgs/applications/science/electronics/kicad/unstable.nix b/pkgs/applications/science/electronics/kicad/unstable.nix index 7475170d6a72c..5310da0699e2e 100644 --- a/pkgs/applications/science/electronics/kicad/unstable.nix +++ b/pkgs/applications/science/electronics/kicad/unstable.nix @@ -52,5 +52,6 @@ stdenv.mkDerivation rec { license = licenses.gpl2; maintainers = with maintainers; [ berce ]; platforms = with platforms; linux; + broken = true; }; } diff --git a/pkgs/applications/science/electronics/librepcb/default.nix b/pkgs/applications/science/electronics/librepcb/default.nix index fb931ec916223..da10ca34b8795 100644 --- a/pkgs/applications/science/electronics/librepcb/default.nix +++ b/pkgs/applications/science/electronics/librepcb/default.nix @@ -1,20 +1,20 @@ -{ stdenv, fetchFromGitHub, qtbase, qttools, qmake }: +{ stdenv, fetchFromGitHub, qtbase, qttools, qmake, wrapQtAppsHook }: stdenv.mkDerivation { pname = "librepcb"; - version = "0.1.0"; + version = "0.1.2"; src = fetchFromGitHub { owner = "LibrePCB"; repo = "LibrePCB"; fetchSubmodules = true; - rev = "d7458d3b3e126499902e1a66a0ef889f516a7c97"; - sha256 = "19wh0398fzzpd65nh4mmc4jllkrgcrwxvxdby0gb5wh1sqyaqac4"; + rev = "acdd94d9d2310f79215125b999153e9da88a9376"; + sha256 = "1bbl01rp75sl6k1cmch7x90v00lck578xvqmb856s9fx75bdgnv5"; }; enableParallelBuilding = true; - nativeBuildInputs = [ qmake qttools ]; + nativeBuildInputs = [ qmake qttools wrapQtAppsHook ]; buildInputs = [ qtbase ]; @@ -25,6 +25,10 @@ stdenv.mkDerivation { cp share/librepcb/fontobene/newstroke.bene $out/share/librepcb/fontobene/ ''; + preFixup = '' + wrapQtApp $out/bin/librepcb + ''; + meta = with stdenv.lib; { description = "A free EDA software to develop printed circuit boards"; homepage = https://librepcb.org/; diff --git a/pkgs/applications/science/logic/hol_light/default.nix b/pkgs/applications/science/logic/hol_light/default.nix index 40b0115dc1b72..cda3656dc59ea 100644 --- a/pkgs/applications/science/logic/hol_light/default.nix +++ b/pkgs/applications/science/logic/hol_light/default.nix @@ -21,13 +21,13 @@ let in stdenv.mkDerivation { - name = "hol_light-2019-03-27"; + name = "hol_light-2019-10-06"; src = fetchFromGitHub { owner = "jrh13"; repo = "hol-light"; - rev = "a2b487b38d9da47350f1b4316e34a8fa4cf7a40a"; - sha256 = "1qlidl15qi8w4si8wxcmj8yg2srsb0q4k1ad9yd91sgx9h9aq8fk"; + rev = "5c91b2ded8a66db571824ecfc18b4536c103b23e"; + sha256 = "0sxsk8z08ba0q5aixdyczcx5l29lb51ba4ip3d2fry7y604kjsx6"; }; buildInputs = [ ocaml camlp5 ]; diff --git a/pkgs/applications/science/logic/jonprl/default.nix b/pkgs/applications/science/logic/jonprl/default.nix index 61ca78d85ed1b..e503836098f19 100644 --- a/pkgs/applications/science/logic/jonprl/default.nix +++ b/pkgs/applications/science/logic/jonprl/default.nix @@ -30,5 +30,6 @@ stdenv.mkDerivation rec { license = stdenv.lib.licenses.mit; maintainers = with stdenv.lib.maintainers; [ puffnfresh ]; platforms = stdenv.lib.platforms.linux; + broken = true; }; } diff --git a/pkgs/applications/science/logic/lean2/default.nix b/pkgs/applications/science/logic/lean2/default.nix index 8cc50bb5e2957..612c9d6f92a2c 100644 --- a/pkgs/applications/science/logic/lean2/default.nix +++ b/pkgs/applications/science/logic/lean2/default.nix @@ -32,5 +32,6 @@ stdenv.mkDerivation { license = licenses.asl20; platforms = platforms.unix; maintainers = with maintainers; [ thoughtpolice gebner ]; + broken = true; }; } diff --git a/pkgs/applications/science/logic/monosat/default.nix b/pkgs/applications/science/logic/monosat/default.nix index 30d47687a3eb7..fba3bc4790607 100644 --- a/pkgs/applications/science/logic/monosat/default.nix +++ b/pkgs/applications/science/logic/monosat/default.nix @@ -39,6 +39,7 @@ let platforms = platforms.unix; license = if includeGplCode then licenses.gpl2 else licenses.mit; homepage = https://github.com/sambayless/monosat; + broken = true; }; }; @@ -64,4 +65,4 @@ let --replace '../../../../libmonosat.so' '${core}/lib/libmonosat.so' ''; }; -in core \ No newline at end of file +in core diff --git a/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix index 8f38a24f40d11..0ab4c1699449a 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 = "5-0-535-0"; + version = "5-0-560-0"; 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 = "1mbjwa9isw390i0k1yh6r9wmh8zkczian0v25w2vxb2a8vv0hjk0"; + sha256 = "16w6z3axzb9g51w4cbyf5zj6gpm9qab65xbw1184v5wym5llf4iw"; }; srcIcon = fetchurl { diff --git a/pkgs/applications/science/math/nasc/default.nix b/pkgs/applications/science/math/nasc/default.nix index c2f8ba1d55ec8..a492178595681 100644 --- a/pkgs/applications/science/math/nasc/default.nix +++ b/pkgs/applications/science/math/nasc/default.nix @@ -1,6 +1,7 @@ { stdenv , fetchFromGitHub , pkgconfig +, vala , gtk3 , glib , pantheon @@ -26,7 +27,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake - pantheon.vala + vala pkgconfig wrapGAppsHook ]; diff --git a/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/pkgs/applications/science/robotics/qgroundcontrol/default.nix index 1863757adbcf8..f9fea3f314625 100644 --- a/pkgs/applications/science/robotics/qgroundcontrol/default.nix +++ b/pkgs/applications/science/robotics/qgroundcontrol/default.nix @@ -69,5 +69,6 @@ stdenv.mkDerivation rec { license = licenses.gpl3Plus; platforms = platforms.linux; maintainers = with maintainers; [ pxc ]; + broken = true; }; } |