Merge branch 'master' into rename-z77z-into-maggesi

19 files changed, 76 insertions, 22 deletions

diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix
index ecca9141d9f..59c6a02d349 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 dbcfead6b1e..696162d2dc5 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 00000000000..bfdf5a1bb17
--- /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 161188f7ef1..fe6919656d9 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/star/default.nix b/pkgs/applications/science/biology/star/default.nix
index f32dca86bdf..8cd23fe06ed 100644
--- a/pkgs/applications/science/biology/star/default.nix
+++ b/pkgs/applications/science/biology/star/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "star";
-  version = "2.7.1a";
+  version = "2.7.2b";
 
   src = fetchFromGitHub {
     repo = "STAR";
     owner = "alexdobin";
     rev = version;
-    sha256 = "0n6g4s4hgw7qygs1z97j7a2dgz8gfaa4cv5pjvvvmarvk0x07hyg";
+    sha256 = "1fb63n3jm1l8k60wdjbq9asv4l1kf7algxxs1aqzvvidx3a8fvzq";
   };
 
   sourceRoot = "source/source";
diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix
index 84c90d89556..c791e8ef89b 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 1fc387fcc66..b1bd01fb2f7 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/eagle/eagle.nix b/pkgs/applications/science/electronics/eagle/eagle.nix
index 2b28f2c06db..7789f4cf8ba 100644
--- a/pkgs/applications/science/electronics/eagle/eagle.nix
+++ b/pkgs/applications/science/electronics/eagle/eagle.nix
@@ -13,11 +13,11 @@ let
   in
   stdenv.mkDerivation rec {
     pname = "eagle";
-    version = "9.4.2";
+    version = "9.5.0";
 
     src = fetchurl {
       url = "https://eagle-updates.circuits.io/downloads/${builtins.replaceStrings ["."] ["_"] version}/Autodesk_EAGLE_${version}_English_Linux_64bit.tar.gz";
-      sha256 = "0lrwrvqcb91mcggmicvwjrngccsdy0f06l7a8nfgp9ckn4d9vmg2";
+      sha256 = "0wakaja98mkdgcxp18d7499i0254ns1xhnx4bag2lqi7j8qn8rqy";
     };
 
     desktopItem = makeDesktopItem {
diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix
index 8dffe580cc6..64c1c3daba8 100644
--- a/pkgs/applications/science/electronics/gtkwave/default.nix
+++ b/pkgs/applications/science/electronics/gtkwave/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gtkwave";
-  version = "3.3.101";
+  version = "3.3.102";
 
   src = fetchurl {
     url    = "mirror://sourceforge/gtkwave/${pname}-${version}.tar.gz";
-    sha256 = "1j6capxwgi8aj3sgqg1r7161icni9y8y93g1rl3bzd3s40jcyhsz";
+    sha256 = "1izyfx6b1n9nr08c7q0gkgcf0q04bb4qz92ckwh74n5l5nwprfw0";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/applications/science/electronics/kicad/unstable.nix b/pkgs/applications/science/electronics/kicad/unstable.nix
index 7475170d6a7..5310da0699e 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 fb931ec9162..da10ca34b87 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 dc08b59bc91..d799b52d115 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 61ca78d85ed..e503836098f 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 8cc50bb5e29..612c9d6f92a 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 30d47687a3e..fba3bc47906 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/clp/default.nix b/pkgs/applications/science/math/clp/default.nix
index 0eb57c75692..f91b091439f 100644
--- a/pkgs/applications/science/math/clp/default.nix
+++ b/pkgs/applications/science/math/clp/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl, zlib }:
 
 stdenv.mkDerivation rec {
-  version = "1.17.2";
+  version = "1.17.3";
   pname = "clp";
   src = fetchurl {
     url = "https://www.coin-or.org/download/source/Clp/Clp-${version}.tgz";
-    sha256 = "1fkmgpn0zaraymi6s3isrrscgjxggcs2yjrx7jfy4hb1jacx71zz";
+    sha256 = "0ws515f73vq2p4nzyq0fbnm4zp9a7mjg54szdzvkql5dj51gafx1";
   };
 
   propagatedBuildInputs = [ zlib ];
diff --git a/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix
index 8f38a24f40d..0ab4c169944 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 c2f8ba1d55e..a4921785956 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 1863757adbc..f9fea3f3146 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;
   };
 }