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-rw-r--r--pkgs/applications/audio/elisa/default.nix4
-rw-r--r--pkgs/applications/audio/openmpt123/default.nix4
-rw-r--r--pkgs/applications/audio/pulseeffects/default.nix4
-rw-r--r--pkgs/applications/audio/qjackctl/default.nix4
-rw-r--r--pkgs/applications/audio/timemachine/default.nix4
-rw-r--r--pkgs/applications/blockchains/bitcoin-abc.nix4
-rw-r--r--pkgs/applications/editors/glow/default.nix15
-rw-r--r--pkgs/applications/editors/kdevelop5/kdev-php.nix4
-rw-r--r--pkgs/applications/editors/kdevelop5/kdev-python.nix4
-rw-r--r--pkgs/applications/editors/kdevelop5/kdevelop.nix4
-rw-r--r--pkgs/applications/editors/neovim/neovim-remote.nix4
-rw-r--r--pkgs/applications/editors/neovim/wrapper.nix2
-rw-r--r--pkgs/applications/editors/quilter/default.nix4
-rw-r--r--pkgs/applications/editors/vscode/vscode.nix2
-rw-r--r--pkgs/applications/editors/vscode/vscodium.nix2
-rw-r--r--pkgs/applications/graphics/azpainter/default.nix4
-rw-r--r--pkgs/applications/graphics/gcolor2/default.nix3
-rw-r--r--pkgs/applications/graphics/gscan2pdf/default.nix4
-rw-r--r--pkgs/applications/graphics/photoqt/default.nix4
-rw-r--r--pkgs/applications/misc/dbeaver/default.nix4
-rw-r--r--pkgs/applications/misc/formatter/default.nix4
-rw-r--r--pkgs/applications/misc/gallery-dl/default.nix4
-rw-r--r--pkgs/applications/misc/heimer/default.nix4
-rw-r--r--pkgs/applications/misc/hugo/default.nix4
-rw-r--r--pkgs/applications/misc/jgmenu/default.nix4
-rw-r--r--pkgs/applications/misc/josm/default.nix4
-rw-r--r--pkgs/applications/misc/khal/default.nix18
-rw-r--r--pkgs/applications/misc/khal/skip-broken-test.patch21
-rw-r--r--pkgs/applications/misc/latte-dock/default.nix4
-rw-r--r--pkgs/applications/misc/pgmodeler/default.nix4
-rw-r--r--pkgs/applications/networking/instant-messengers/quaternion/default.nix6
-rw-r--r--pkgs/applications/networking/p2p/gnunet/default.nix4
-rw-r--r--pkgs/applications/office/tusk/default.nix54
-rw-r--r--pkgs/applications/science/biology/blast/default.nix108
-rw-r--r--pkgs/applications/science/biology/blast/no_slash_bin.patch184
-rw-r--r--pkgs/applications/science/biology/last/default.nix4
-rw-r--r--pkgs/applications/science/chemistry/openmolcas/default.nix16
-rw-r--r--pkgs/applications/science/math/geogebra/default.nix4
-rw-r--r--pkgs/applications/science/molecular-dynamics/gromacs/default.nix6
-rw-r--r--pkgs/applications/version-management/cvs-fast-export/default.nix6
-rw-r--r--pkgs/applications/version-management/git-and-tools/git-machete/default.nix4
-rw-r--r--pkgs/applications/version-management/git-and-tools/gitstatus/default.nix6
-rw-r--r--pkgs/applications/version-management/git-and-tools/gitstatus/romkatv_libgit2.nix4
-rw-r--r--pkgs/applications/version-management/mercurial/4.9.nix71
-rw-r--r--pkgs/applications/virtualization/conmon/default.nix4
-rw-r--r--pkgs/applications/virtualization/podman/default.nix4
-rw-r--r--pkgs/applications/window-managers/cwm/default.nix4
47 files changed, 552 insertions, 92 deletions
diff --git a/pkgs/applications/audio/elisa/default.nix b/pkgs/applications/audio/elisa/default.nix
index 37c95430627..fdfca08c0b0 100644
--- a/pkgs/applications/audio/elisa/default.nix
+++ b/pkgs/applications/audio/elisa/default.nix
@@ -7,13 +7,13 @@
 
 mkDerivation rec {
   pname = "elisa";
-  version = "0.4.2";
+  version = "19.12.0";
 
   src = fetchFromGitHub {
     owner  = "KDE";
     repo   = "elisa";
     rev    = "v${version}";
-    sha256 = "0q098zaajwbpkrarrsdzpjhpsq2nxkqaxwzhr2gjlg08j9vqkpfm";
+    sha256 = "1939xwhy1s502pai63vz56hnnsl3qsb6arhrlg5bw6bwsv88blac";
   };
 
   buildInputs = [ vlc ];
diff --git a/pkgs/applications/audio/openmpt123/default.nix b/pkgs/applications/audio/openmpt123/default.nix
index 0e52d144e51..24ac52e7e31 100644
--- a/pkgs/applications/audio/openmpt123/default.nix
+++ b/pkgs/applications/audio/openmpt123/default.nix
@@ -2,14 +2,14 @@
 , usePulseAudio ? config.pulseaudio or false, libpulseaudio }:
 
 let
-  version = "0.4.10";
+  version = "0.4.11";
 in stdenv.mkDerivation {
   pname = "openmpt123";
   inherit version;
 
   src = fetchurl {
     url = "https://lib.openmpt.org/files/libopenmpt/src/libopenmpt-${version}+release.autotools.tar.gz";
-    sha256 = "12i5iwxb5g27amqgqr6iiy63w49nwil5vyypnbj91ahy97ah8a3a";
+    sha256 = "1g96bpwh419s429wb387lkmhjsn3ldsjrzrb8h9p3wva5z6943i6";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/applications/audio/pulseeffects/default.nix b/pkgs/applications/audio/pulseeffects/default.nix
index 2d941f74c73..31e19154862 100644
--- a/pkgs/applications/audio/pulseeffects/default.nix
+++ b/pkgs/applications/audio/pulseeffects/default.nix
@@ -46,13 +46,13 @@ let
   ];
 in stdenv.mkDerivation rec {
   pname = "pulseeffects";
-  version = "4.6.9";
+  version = "4.7.0";
 
   src = fetchFromGitHub {
     owner = "wwmm";
     repo = "pulseeffects";
     rev = "v${version}";
-    sha256 = "0ag19hvf50ip7z1s8jziy4pm8c72w7qq9zzgb4967l6v17rar4yh";
+    sha256 = "1cpiill24c54sy97xm1r0sqqpxj6ar40pnnwb72qs8b9zzci920r";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/audio/qjackctl/default.nix b/pkgs/applications/audio/qjackctl/default.nix
index 84cc11b8bf3..753f6fe8206 100644
--- a/pkgs/applications/audio/qjackctl/default.nix
+++ b/pkgs/applications/audio/qjackctl/default.nix
@@ -1,14 +1,14 @@
 { stdenv, mkDerivation, fetchurl, pkgconfig, alsaLib, libjack2, dbus, qtbase, qttools, qtx11extras }:
 
 mkDerivation rec {
-  version = "0.6.0";
+  version = "0.6.1";
   pname = "qjackctl";
 
   # some dependencies such as killall have to be installed additionally
 
   src = fetchurl {
     url = "mirror://sourceforge/qjackctl/${pname}-${version}.tar.gz";
-    sha256 = "1kddvxxhwvw1ps1c1drr08hxqci7jw4jwr8h1d9isb8agydfxmcx";
+    sha256 = "09y0s43ypcghnvzsz89mi1qs5bsvn4hpb98lqxmwwsy0ikcv3hny";
   };
 
   buildInputs = [
diff --git a/pkgs/applications/audio/timemachine/default.nix b/pkgs/applications/audio/timemachine/default.nix
index 48dd3f39e88..3564f875c9b 100644
--- a/pkgs/applications/audio/timemachine/default.nix
+++ b/pkgs/applications/audio/timemachine/default.nix
@@ -4,12 +4,12 @@
 
 stdenv.mkDerivation rec {
   pname = "timemachine";
-  version = "0.3.3";
+  version = "0.3.4";
   src = fetchFromGitHub {
     owner = "swh";
     repo = "timemachine";
     rev = "v${version}";
-    sha256 = "1jsvd29wiqigxyqxl2xjklla11fwyjy68vqivcnlr9f2af4ylym8";
+    sha256 = "16fgyw6jnscx9279dczv72092dddghwlp53rkfw469kcgvjhwx0z";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/applications/blockchains/bitcoin-abc.nix b/pkgs/applications/blockchains/bitcoin-abc.nix
index d872204c6b0..85d6dcbdbe6 100644
--- a/pkgs/applications/blockchains/bitcoin-abc.nix
+++ b/pkgs/applications/blockchains/bitcoin-abc.nix
@@ -7,13 +7,13 @@ with stdenv.lib;
 mkDerivation rec {
 
   name = "bitcoin" + (toString (optional (!withGui) "d")) + "-abc-" + version;
-  version = "0.20.8";
+  version = "0.20.9";
 
   src = fetchFromGitHub {
     owner = "bitcoin-ABC";
     repo = "bitcoin-abc";
     rev = "v${version}";
-    sha256 = "0srjc11i7azqn3flipjwzm67w20ji24yslkmchy1a834fyb1gmx1";
+    sha256 = "1dmk7vm4r9n0yia8dazlx4fmr8i1r8cz8p1pj11glpa3pwda3669";
   };
 
   patches = [ ./fix-bitcoin-qt-build.patch ];
diff --git a/pkgs/applications/editors/glow/default.nix b/pkgs/applications/editors/glow/default.nix
index 0e30d879b0c..7187a2df80c 100644
--- a/pkgs/applications/editors/glow/default.nix
+++ b/pkgs/applications/editors/glow/default.nix
@@ -2,20 +2,23 @@
 
 buildGoModule rec {
   pname = "glow";
-  version = "0.1.3";
+  version = "0.1.6";
 
   src = fetchFromGitHub {
     owner = "charmbracelet";
     repo = "glow";
     rev = "v${version}";
-    sha256 = "16zadrp42y01hi83hg47cw6c9zpw8z4xfssb5pxkmd2ynihaxfv5";
+    sha256 = "0q35napi1aa6dfrqz26hvhzijymb9sxsf3mrrn1mh7ssgkhvmqqc";
   };
 
-  modSha256 = "1q67j9wg0kgb41zjgdbcrywxbwh597n8shwnwgl2xa6f7fvzpr4f";
+  modSha256 = "07imn9p0s79x1h45dk05hjcm6946d84j6k5pnljqrz4zk64hy26c";
 
-  meta = src.meta // {
+  buildFlagsArray = [ "-ldflags=" "-X=main.Version=${version}" ];
+
+  meta = with lib; {
     description = "Render markdown on the CLI";
-    maintainers = with lib.maintainers; [ ehmry filalex77 ];
-    license = lib.licenses.mit;
+    homepage = "https://github.com/charmbracelet/glow";
+    license = licenses.mit;
+    maintainers = with maintainers; [ ehmry filalex77 ];
   };
 }
diff --git a/pkgs/applications/editors/kdevelop5/kdev-php.nix b/pkgs/applications/editors/kdevelop5/kdev-php.nix
index 19fef1c42dc..35efe76cfb2 100644
--- a/pkgs/applications/editors/kdevelop5/kdev-php.nix
+++ b/pkgs/applications/editors/kdevelop5/kdev-php.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "kdev-php";
-  version = "5.4.5";
+  version = "5.4.6";
 
   src = fetchurl {
     url = "https://github.com/KDE/${pname}/archive/v${version}.tar.gz";
-    sha256 = "12j0l2k6ii9ajp90lil3apk0xsz56cb549ighabik73a1w3c6ib6";
+    sha256 = "0p532r0ld6j6fpwqyf9m5m0d27y37chgbvcjp1x6g5jjvm7m77xk";
   };
 
   nativeBuildInputs = [ cmake extra-cmake-modules ];
diff --git a/pkgs/applications/editors/kdevelop5/kdev-python.nix b/pkgs/applications/editors/kdevelop5/kdev-python.nix
index 7723b9482a2..0f15a63be7a 100644
--- a/pkgs/applications/editors/kdevelop5/kdev-python.nix
+++ b/pkgs/applications/editors/kdevelop5/kdev-python.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "kdev-python";
-  version = "5.4.5";
+  version = "5.4.6";
 
   src = fetchurl {
     url = "https://github.com/KDE/${pname}/archive/v${version}.tar.gz";
-    sha256 = "1iq4lxbl8gq4qvydyz34ild4izw21cp22adlz9dc054v0wis331j";
+    sha256 = "1xzk0zgbc4nnz8gjbhw5h6kwznzxsqrg19ggyb8ijpmgg0ncxk8l";
   };
 
   cmakeFlags = [
diff --git a/pkgs/applications/editors/kdevelop5/kdevelop.nix b/pkgs/applications/editors/kdevelop5/kdevelop.nix
index 21b469347df..ed5017a0487 100644
--- a/pkgs/applications/editors/kdevelop5/kdevelop.nix
+++ b/pkgs/applications/editors/kdevelop5/kdevelop.nix
@@ -10,11 +10,11 @@
 
 mkDerivation rec {
   pname = "kdevelop";
-  version = "5.4.5";
+  version = "5.4.6";
 
   src = fetchurl {
     url = "mirror://kde/stable/${pname}/${version}/src/${pname}-${version}.tar.xz";
-    sha256 = "08vhbg9ql0402bw3y3xw1kdxhig9sv3ss8g0h4477vy3z17m1h4j";
+    sha256 = "01jmrmwbc1hrvq7jdfcc7mxl03q2l6kz57yca2j26xwyvfcfv5sz";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/editors/neovim/neovim-remote.nix b/pkgs/applications/editors/neovim/neovim-remote.nix
index 9893c6085a6..aae37b5a262 100644
--- a/pkgs/applications/editors/neovim/neovim-remote.nix
+++ b/pkgs/applications/editors/neovim/neovim-remote.nix
@@ -4,14 +4,14 @@ with stdenv.lib;
 
 pythonPackages.buildPythonApplication rec {
   pname = "neovim-remote";
-  version = "2.2.3";
+  version = "2.4.0";
   disabled = !pythonPackages.isPy3k;
 
   src = fetchFromGitHub {
     owner = "mhinz";
     repo = "neovim-remote";
     rev = "v${version}";
-    sha256 = "0g7gs5gigk3krydxdpmscgfr1fms0a6rc6am2y4c5szkgbd1d0ph";
+    sha256 = "0jlw0qksak4bdzddpsj74pm2f2bgpj3cwrlspdjjy0j9qzg0mpl9";
   };
 
   propagatedBuildInputs = with pythonPackages; [ pynvim psutil ];
diff --git a/pkgs/applications/editors/neovim/wrapper.nix b/pkgs/applications/editors/neovim/wrapper.nix
index ffe597b00db..c0b97667757 100644
--- a/pkgs/applications/editors/neovim/wrapper.nix
+++ b/pkgs/applications/editors/neovim/wrapper.nix
@@ -101,7 +101,7 @@ let
         # Only display the log on error since it will contain a few normally
         # irrelevant messages.
         if ! $out/bin/nvim \
-          -u ${vimUtils.vimrcFile (configure // { customRC = ""; beforePlugins = ''filetype indent plugin on | syn on''; })} \
+          -u ${vimUtils.vimrcFile (configure // { customRC = ""; })} \
           -i NONE -n \
           -E -V1rplugins.log -s \
           +UpdateRemotePlugins +quit! > outfile 2>&1; then
diff --git a/pkgs/applications/editors/quilter/default.nix b/pkgs/applications/editors/quilter/default.nix
index 668c8d740b2..ceb119a5f0a 100644
--- a/pkgs/applications/editors/quilter/default.nix
+++ b/pkgs/applications/editors/quilter/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "quilter";
-  version = "2.0.4";
+  version = "2.0.5";
 
   src = fetchFromGitHub {
     owner = "lainsce";
     repo = pname;
     rev = version;
-    sha256 = "1vbckx4c2bklzxpqz332sjcyrx1xl1j0cp8778fvpl7x7mlnz460";
+    sha256 = "1gij5gqidzvwym7yq5fx0344n4fkydx5diwz8g8kwkcsz7z1w45a";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/editors/vscode/vscode.nix b/pkgs/applications/editors/vscode/vscode.nix
index d602647c34c..663c64ac5de 100644
--- a/pkgs/applications/editors/vscode/vscode.nix
+++ b/pkgs/applications/editors/vscode/vscode.nix
@@ -16,6 +16,8 @@ let
   }.${system};
 in
   callPackage ./generic.nix rec {
+    # The update script doesn't correctly change the hash for darwin, so please:
+    # nixpkgs-update: no auto update
 
     version = "1.41.1";
     pname = "vscode";
diff --git a/pkgs/applications/editors/vscode/vscodium.nix b/pkgs/applications/editors/vscode/vscodium.nix
index 72484730a3e..e7bdacc1390 100644
--- a/pkgs/applications/editors/vscode/vscodium.nix
+++ b/pkgs/applications/editors/vscode/vscodium.nix
@@ -22,6 +22,8 @@ let
 in
   callPackage ./generic.nix rec {
     inherit sourceRoot;
+    # The update script doesn't correctly change the hash for darwin, so please:
+    # nixpkgs-update: no auto update
 
     version = "1.41.1";
     pname = "vscodium";
diff --git a/pkgs/applications/graphics/azpainter/default.nix b/pkgs/applications/graphics/azpainter/default.nix
index b2060f5db31..2f636764e1f 100644
--- a/pkgs/applications/graphics/azpainter/default.nix
+++ b/pkgs/applications/graphics/azpainter/default.nix
@@ -7,13 +7,13 @@
 
 stdenv.mkDerivation rec {
   pname = "azpainter";
-  version = "2.1.4";
+  version = "2.1.5";
 
   src = fetchFromGitHub {
     owner = "Symbian9";
     repo = pname;
     rev = "refs/tags/v${version}";
-    sha256 = "1hrr9lhsbjyzar3nxvli6cazr7zhyzh0p8hwpg4g9ga6njs8vi8m";
+    sha256 = "0x5jmsprjissqcvwq75pqq9wgv4k9b7cy507hai8xk6xs3vxwgba";
   };
 
   nativeBuildInputs = [ autoreconfHook ];
diff --git a/pkgs/applications/graphics/gcolor2/default.nix b/pkgs/applications/graphics/gcolor2/default.nix
index 2762748bc1a..f729c9c2bba 100644
--- a/pkgs/applications/graphics/gcolor2/default.nix
+++ b/pkgs/applications/graphics/gcolor2/default.nix
@@ -8,8 +8,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url = "mirror://sourceforge/project/gcolor2/gcolor2/${version}/gcolor2-${version}.tar.bz2";
-    sha1 = "e410a52dcff3d5c6c3d448b68a026d04ccd744be";
-
+    sha256 = "1siv54vwx9dbfcflklvf7pkp5lk6h3nn63flg6jzifz9wp0c84q6";
   };
 
   preConfigure = ''
diff --git a/pkgs/applications/graphics/gscan2pdf/default.nix b/pkgs/applications/graphics/gscan2pdf/default.nix
index f8d50a7c798..76bb0bc1317 100644
--- a/pkgs/applications/graphics/gscan2pdf/default.nix
+++ b/pkgs/applications/graphics/gscan2pdf/default.nix
@@ -10,11 +10,11 @@ with stdenv.lib;
 
 perlPackages.buildPerlPackage rec {
   pname = "gscan2pdf";
-  version = "2.6.2";
+  version = "2.6.3";
 
   src = fetchurl {
     url = "mirror://sourceforge/gscan2pdf/${version}/${pname}-${version}.tar.xz";
-    sha256 = "0z35lglf4anfczizynjp8sd1jpix5mkmm1nh39n1v94l7ahjxsww";
+    sha256 = "1chmk51xwylnjrgc6hw23x7g7cpwzgwmjc49fcah7pkd3dk1cvvr";
   };
 
   nativeBuildInputs = [ wrapGAppsHook ];
diff --git a/pkgs/applications/graphics/photoqt/default.nix b/pkgs/applications/graphics/photoqt/default.nix
index 68afdd8694b..14c49d30004 100644
--- a/pkgs/applications/graphics/photoqt/default.nix
+++ b/pkgs/applications/graphics/photoqt/default.nix
@@ -1,9 +1,9 @@
-{ stdenv, fetchurl, cmake, exiv2, graphicsmagick, libraw, fetchpatch
+{ mkDerivation, stdenv, fetchurl, cmake, exiv2, graphicsmagick, libraw, fetchpatch
 , qtbase, qtdeclarative, qtmultimedia, qtquickcontrols, qttools, qtgraphicaleffects
 , extra-cmake-modules, poppler, kimageformats, libarchive, libdevil
 }:
 
-stdenv.mkDerivation rec {
+mkDerivation rec {
   pname = "photoqt";
   version = "1.7.1";
 
diff --git a/pkgs/applications/misc/dbeaver/default.nix b/pkgs/applications/misc/dbeaver/default.nix
index dfb9e1dd921..d0011eee9c1 100644
--- a/pkgs/applications/misc/dbeaver/default.nix
+++ b/pkgs/applications/misc/dbeaver/default.nix
@@ -7,7 +7,7 @@
 
 stdenv.mkDerivation rec {
   pname = "dbeaver-ce";
-  version = "6.3.1";
+  version = "6.3.2";
 
   desktopItem = makeDesktopItem {
     name = "dbeaver";
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://dbeaver.io/files/${version}/dbeaver-ce-${version}-linux.gtk.x86_64.tar.gz";
-    sha256 = "0w7nsxm66gbwwql1zk7zh6zvvsjcn78qm0miv0w8nj1qk24zr494";
+    sha256 = "0yr79p4vdg6s6c8sry6qnf2ifjcjdapn0sff2crsnz331rsh27sm";
   };
 
   installPhase = ''
diff --git a/pkgs/applications/misc/formatter/default.nix b/pkgs/applications/misc/formatter/default.nix
index 7cb1e7dfebb..b777c3b72e7 100644
--- a/pkgs/applications/misc/formatter/default.nix
+++ b/pkgs/applications/misc/formatter/default.nix
@@ -20,13 +20,13 @@
 
 stdenv.mkDerivation rec {
   pname = "formatter";
-  version = "0.3.1";
+  version = "0.3.2";
 
   src = fetchFromGitHub {
     owner = "Djaler";
     repo = "Formatter";
     rev = version;
-    sha256 = "1ghxd2h0pklhlrjslfr46vza1kjsm3mr0sdzzjiqi9jd6hddnk7i";
+    sha256 = "0da1dvzsvbwg1ys19yf0n080xc0hjwin9zacjndb24jvphy3bxql";
   };
 
   patches = [
diff --git a/pkgs/applications/misc/gallery-dl/default.nix b/pkgs/applications/misc/gallery-dl/default.nix
index b27e456e966..d578479787b 100644
--- a/pkgs/applications/misc/gallery-dl/default.nix
+++ b/pkgs/applications/misc/gallery-dl/default.nix
@@ -2,11 +2,11 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "gallery_dl";
-  version = "1.12.1";
+  version = "1.12.2";
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "0y1bzqcacik030zjchgmzrwpfb49mi68wdivli9ydb64w1zql9im";
+    sha256 = "013bavyqvnay38c844n1jvirsmj807f0wg2qlclkdghkj316p1pz";
   };
 
   doCheck = false;
diff --git a/pkgs/applications/misc/heimer/default.nix b/pkgs/applications/misc/heimer/default.nix
index 39ae0e04670..5f403c9b7b6 100644
--- a/pkgs/applications/misc/heimer/default.nix
+++ b/pkgs/applications/misc/heimer/default.nix
@@ -2,13 +2,13 @@
 
 mkDerivation rec {
   pname = "heimer";
-  version = "1.12.0";
+  version = "1.13.1";
 
   src = fetchFromGitHub {
     owner = "juzzlin";
     repo = pname;
     rev = version;
-    sha256 = "1gw4w6cvr3vb4zdb1kq8gwmadh2lb0jd0bd2hc7cw2d5kdbjaln7";
+    sha256 = "1s6s5rlzr917hq7370pmikbdvd6y468cyxw614ah65d4v105qfv7";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/applications/misc/hugo/default.nix b/pkgs/applications/misc/hugo/default.nix
index b5c57054f8b..69ca6a83764 100644
--- a/pkgs/applications/misc/hugo/default.nix
+++ b/pkgs/applications/misc/hugo/default.nix
@@ -2,7 +2,7 @@
 
 buildGoModule rec {
   pname = "hugo";
-  version = "0.62.0";
+  version = "0.62.2";
 
   goPackagePath = "github.com/gohugoio/hugo";
 
@@ -10,7 +10,7 @@ buildGoModule rec {
     owner = "gohugoio";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0z14qhsjgwqgm7kj25y0zh4b42bwd7zhcmwjxzkk6chzw7fwq375";
+    sha256 = "1rdfx5gv0q64ivyg0ilb96p5nksip9cj75fmvw0bjky9w6i07yd9";
   };
 
   modSha256 = "0dwv5qnglv00jj7vlps76zlfpkzsplf93401j2l03xfvmvadifrs";
diff --git a/pkgs/applications/misc/jgmenu/default.nix b/pkgs/applications/misc/jgmenu/default.nix
index 31568c7b0fd..cbe26b817e2 100644
--- a/pkgs/applications/misc/jgmenu/default.nix
+++ b/pkgs/applications/misc/jgmenu/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "jgmenu";
-  version = "3.5";
+  version = "4.0";
 
   src = fetchFromGitHub {
     owner = "johanmalm";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0q0m3sskgmjv28gzvjkphgg3yhwzc9w9fj9i342pibb50impjazy";
+    sha256 = "1s9291y38k4adc2wqj7plfhj431nf36zs262jm6mmb2fs910ncgv";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/misc/josm/default.nix b/pkgs/applications/misc/josm/default.nix
index be620192dc3..ac46c48d407 100644
--- a/pkgs/applications/misc/josm/default.nix
+++ b/pkgs/applications/misc/josm/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "josm";
-  version = "15553";
+  version = "15628";
 
   src = fetchurl {
     url = "https://josm.openstreetmap.de/download/josm-snapshot-${version}.jar";
-    sha256 = "07kkc19r9xkb5jim26nnmajp0jzvg3absgx55z5qnna6r189ba2j";
+    sha256 = "19yn311h9x1434832i0awpv2n9vhbhkk1j1mi9zggy9f256f80c6";
   };
 
   buildInputs = [ jdk11 makeWrapper ];
diff --git a/pkgs/applications/misc/khal/default.nix b/pkgs/applications/misc/khal/default.nix
index 756c8e25971..c435eaefed5 100644
--- a/pkgs/applications/misc/khal/default.nix
+++ b/pkgs/applications/misc/khal/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, pkgs, python3, fetchpatch }:
+{ stdenv, pkgs, python3, fetchpatch, glibcLocales }:
 
 with python3.pkgs; buildPythonApplication rec {
   pname = "khal";
@@ -11,11 +11,14 @@ with python3.pkgs; buildPythonApplication rec {
 
   # Include a khal.desktop file via upstream commit.
   # This patch should be removed when updating to the next version, probably.
-  patches = [ (fetchpatch {
-    name = "add-khal-dot-desktop.patch";
-    url = "https://github.com/pimutils/khal/commit/1f93d238fec7c934dd2f8e48f54925d22130e3aa.patch";
-    sha256 = "06skn3van7zd93348fc6axllx71ckkc7h2zljqlvwa339vca608c";
-  }) ];
+  patches = [
+    (fetchpatch {
+      name = "add-khal-dot-desktop.patch";
+      url = "https://github.com/pimutils/khal/commit/1f93d238fec7c934dd2f8e48f54925d22130e3aa.patch";
+      sha256 = "06skn3van7zd93348fc6axllx71ckkc7h2zljqlvwa339vca608c";
+    })
+    ./skip-broken-test.patch
+  ];
 
   propagatedBuildInputs = [
     atomicwrites
@@ -35,7 +38,8 @@ with python3.pkgs; buildPythonApplication rec {
     freezegun
   ];
   nativeBuildInputs = [ setuptools_scm sphinx sphinxcontrib_newsfeed ];
-  checkInputs = [ pytest ];
+  checkInputs = [ pytest glibcLocales ];
+  LC_ALL = "en_US.UTF-8";
 
   postInstall = ''
     # zsh completion
diff --git a/pkgs/applications/misc/khal/skip-broken-test.patch b/pkgs/applications/misc/khal/skip-broken-test.patch
new file mode 100644
index 00000000000..c3c982547ae
--- /dev/null
+++ b/pkgs/applications/misc/khal/skip-broken-test.patch
@@ -0,0 +1,21 @@
+diff --git a/tests/ui/test_editor.py b/tests/ui/test_editor.py
+index 27b7fa5..5978d72 100644
+--- a/tests/ui/test_editor.py
++++ b/tests/ui/test_editor.py
+@@ -1,5 +1,7 @@
+ import datetime as dt
+ 
++import pytest
++
+ import icalendar
+ from khal.ui.editor import RecurrenceEditor, StartEndEditor
+ 
+@@ -19,7 +21,7 @@ palette = {
+     'edit': 'blue',
+ }
+ 
+-
++@pytest.mark.skip(reason="Mocking breaks in this testcase")
+ def test_popup(monkeypatch):
+     """making sure the popup calendar gets callend with the right inital value
+ 
diff --git a/pkgs/applications/misc/latte-dock/default.nix b/pkgs/applications/misc/latte-dock/default.nix
index f3daedfb96b..d7d23853e11 100644
--- a/pkgs/applications/misc/latte-dock/default.nix
+++ b/pkgs/applications/misc/latte-dock/default.nix
@@ -3,11 +3,11 @@
 
 mkDerivation rec {
   pname = "latte-dock";
-  version = "0.9.5";
+  version = "0.9.7";
 
   src = fetchurl {
     url = "https://download.kde.org/stable/${pname}/${pname}-${version}.tar.xz";
-    sha256 = "1g8a2lmg9agcs2kwbwh6sj9hkrbzad7bkxk39nx5536svnifbg1c";
+    sha256 = "1b8yz6r6x46xajx900m8s0sjfwiwbpp6nfb780ygfcz6inb1234q";
     name = "${pname}-${version}.tar.xz";
   };
 
diff --git a/pkgs/applications/misc/pgmodeler/default.nix b/pkgs/applications/misc/pgmodeler/default.nix
index 5ce7d06d727..83e45e25581 100644
--- a/pkgs/applications/misc/pgmodeler/default.nix
+++ b/pkgs/applications/misc/pgmodeler/default.nix
@@ -4,13 +4,13 @@
 
 mkDerivation rec {
   pname = "pgmodeler";
-  version = "0.9.1";
+  version = "0.9.2";
 
   src = fetchFromGitHub {
     owner = "pgmodeler";
     repo = "pgmodeler";
     rev = "v${version}";
-    sha256 = "15isnbli9jj327r6sj7498nmhgf1mzdyhc1ih120ibw4900aajiv";
+    sha256 = "1wkvg20krfwkziz7skgmwlinx07jm5nl3455payg5brv69zf60kl";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/applications/networking/instant-messengers/quaternion/default.nix b/pkgs/applications/networking/instant-messengers/quaternion/default.nix
index 569c7b68edc..757551c7074 100644
--- a/pkgs/applications/networking/instant-messengers/quaternion/default.nix
+++ b/pkgs/applications/networking/instant-messengers/quaternion/default.nix
@@ -1,6 +1,8 @@
 { mkDerivation, stdenv, lib, fetchFromGitHub, cmake
 , qtbase, qtquickcontrols, qtkeychain, qtmultimedia, qttools
-, libqmatrixclient_0_5 }:
+, libqmatrixclient_0_5
+, gnome3
+}:
 
 let
   generic = version: sha256: prefix: library: mkDerivation {
@@ -14,7 +16,7 @@ let
       inherit sha256;
     };
 
-    buildInputs = [ qtbase qtmultimedia qtquickcontrols qtkeychain library ];
+    buildInputs = [ qtbase qtmultimedia qtquickcontrols qtkeychain library gnome3.libsecret ];
 
     nativeBuildInputs = [ cmake qttools ];
 
diff --git a/pkgs/applications/networking/p2p/gnunet/default.nix b/pkgs/applications/networking/p2p/gnunet/default.nix
index 4967e0e27fe..e4b306453a4 100644
--- a/pkgs/applications/networking/p2p/gnunet/default.nix
+++ b/pkgs/applications/networking/p2p/gnunet/default.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gnunet";
-  version = "0.12.0";
+  version = "0.12.1";
 
   src = fetchurl {
     url = "mirror://gnu/gnunet/${pname}-${version}.tar.gz";
-    sha256 = "1bz0sbhbsivi1bcabk3vpxqnh4vgp86vrmiwkyb5fiqfjviar111";
+    sha256 = "0zhz3dd4mr6k7wlcxw2xclq8p8l4ia5nlg78dylyz6lbz96h2lsm";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/applications/office/tusk/default.nix b/pkgs/applications/office/tusk/default.nix
new file mode 100644
index 00000000000..d54f27f9bbf
--- /dev/null
+++ b/pkgs/applications/office/tusk/default.nix
@@ -0,0 +1,54 @@
+{ appimageTools, fetchurl, lib, gsettings-desktop-schemas, gtk3
+, makeDesktopItem
+}:
+
+let
+  pname = "tusk";
+  version = "0.23.0";
+
+  icon = fetchurl {
+    url = "https://raw.githubusercontent.com/klaussinani/tusk/v${version}/static/Icon.png";
+    sha256 = "1jqclyrjgg6hir45spg75plfmd8k9nrsrzw3plbcg43s5m1qzihb";
+  };
+
+  desktopItem = makeDesktopItem {
+    name = pname;
+    exec = pname;
+    icon = icon;
+    desktopName = pname;
+    genericName = "Evernote desktop app";
+    categories = "Application";
+  };
+
+in appimageTools.wrapType2 rec {
+  name = "${pname}-v${version}";
+  src = fetchurl {
+    url = "https://github.com/klaussinani/tusk/releases/download/v${version}/${pname}-${version}-x86_64.AppImage";
+    sha256 = "02q7wsnhlyq8z74avflrm7805ny8fzlmsmz4bmafp4b4pghjh5ky";
+  };
+
+
+  profile = ''
+    export LC_ALL=C.UTF-8
+    export XDG_DATA_DIRS=${gsettings-desktop-schemas}/share/gsettings-schemas/${gsettings-desktop-schemas.name}:${gtk3}/share/gsettings-schemas/${gtk3.name}:$XDG_DATA_DIRS
+  '';
+
+  multiPkgs = null; # no 32bit needed
+  extraPkgs = appimageTools.defaultFhsEnvArgs.multiPkgs;
+  extraInstallCommands = ''
+    mv $out/bin/{${name},${pname}}
+    mkdir "$out/share"
+    ln -s "${desktopItem}/share/applications" "$out/share/"
+  '';
+
+  meta = with lib; {
+    description = "Refined Evernote desktop app";
+    longDescription = ''
+      Tusk is an unofficial, featureful, open source, community-driven, free Evernote app used by people in more than 140 countries. Tusk is indicated by Evernote as an alternative client for Linux environments trusted by the open source community.
+    '';
+    homepage = "https://klaussinani.github.io/tusk/";
+    license = licenses.mit;
+    maintainers = with maintainers; [ tbenst ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
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 ];
diff --git a/pkgs/applications/version-management/cvs-fast-export/default.nix b/pkgs/applications/version-management/cvs-fast-export/default.nix
index 176e42bbd8a..81b779f0206 100644
--- a/pkgs/applications/version-management/cvs-fast-export/default.nix
+++ b/pkgs/applications/version-management/cvs-fast-export/default.nix
@@ -7,7 +7,7 @@ with stdenv; with lib;
 mkDerivation rec {
   name = "cvs-fast-export-${meta.version}";
   meta = {
-    version = "1.49";
+    version = "1.50";
     description = "Export an RCS or CVS history as a fast-import stream";
     license = licenses.gpl2Plus;
     maintainers = with maintainers; [ dfoxfranke ];
@@ -16,8 +16,8 @@ mkDerivation rec {
   };
 
   src = fetchurl {
-    url = "http://www.catb.org/~esr/cvs-fast-export/cvs-fast-export-1.49.tar.gz";
-    sha256 = "1d75aq6inmd6yvc3rpxw1al95lvbl7wq64v3wygq69prrnzg8b6i";
+    url = "http://www.catb.org/~esr/cvs-fast-export/cvs-fast-export-1.50.tar.gz";
+    sha256 = "01m5l9xnl387hpyik5jvyhghkffj5v1wyxqpxpjxv69q9ly905yk";
   };
 
   buildInputs = [
diff --git a/pkgs/applications/version-management/git-and-tools/git-machete/default.nix b/pkgs/applications/version-management/git-and-tools/git-machete/default.nix
index 92c54dcac6b..6f8c4091a16 100644
--- a/pkgs/applications/version-management/git-and-tools/git-machete/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-machete/default.nix
@@ -4,11 +4,11 @@
 
 buildPythonApplication rec {
   pname = "git-machete";
-  version = "2.12.5";
+  version = "2.12.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1m4j8nhdkr28xs2xbnyy3ric9i99swb4d5drj4wpkqd2xqln5wlq";
+    sha256 = "1h7daf74s0plnqrz2f63s6rak8fmqns96ydjn01366bcsqrbvkw6";
   };
 
   nativeBuildInputs = [ installShellFiles pbr ];
diff --git a/pkgs/applications/version-management/git-and-tools/gitstatus/default.nix b/pkgs/applications/version-management/git-and-tools/gitstatus/default.nix
index bb08516701a..94753275b61 100644
--- a/pkgs/applications/version-management/git-and-tools/gitstatus/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/gitstatus/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation {
   pname = "gitstatus";
-  version = "unstable-2019-05-06";
+  version = "unstable-2019-12-18";
 
   src = fetchFromGitHub {
     owner = "romkatv";
     repo = "gitstatus";
-    rev = "9c791f93c23c04dadfab8b4309a863b62a6ee424";
-    sha256 = "0jbdrgl62x6j920h72n2q6304fb6gdgnmllpv4aa76m13b9qhgq6";
+    rev = "8ae9c17a60158dcf91f56d9167493e3988a5e921";
+    sha256 = "1czjwsgbmxd1d656srs3n6wj6bmqr8p3aw5gw61q4wdxw3mni2a6";
   };
 
   buildInputs = [ (callPackage ./romkatv_libgit2.nix {}) ];
diff --git a/pkgs/applications/version-management/git-and-tools/gitstatus/romkatv_libgit2.nix b/pkgs/applications/version-management/git-and-tools/gitstatus/romkatv_libgit2.nix
index 0ff7fae2878..211ad1eccd8 100644
--- a/pkgs/applications/version-management/git-and-tools/gitstatus/romkatv_libgit2.nix
+++ b/pkgs/applications/version-management/git-and-tools/gitstatus/romkatv_libgit2.nix
@@ -13,7 +13,7 @@ libgit2.overrideAttrs (oldAttrs: {
   src = fetchFromGitHub {
     owner = "romkatv";
     repo = "libgit2";
-    rev = "aab6c56e6766fa752bef00c745067d875925fc89";
-    sha256 = "1yqqhpi5xi6s86411sixw4yq5c6n2v8pdh447c8b7q5lfc089lvl";
+    rev = "75be63625a0de418ec3551306362ee1e21034039";
+    sha256 = "1bwr1ahfxn1nn2f78ri91icxpv8xhpmgypcvg042cmcpm2qrahz9";
   };
 })
diff --git a/pkgs/applications/version-management/mercurial/4.9.nix b/pkgs/applications/version-management/mercurial/4.9.nix
new file mode 100644
index 00000000000..b8fc767bd3a
--- /dev/null
+++ b/pkgs/applications/version-management/mercurial/4.9.nix
@@ -0,0 +1,71 @@
+{ stdenv, fetchurl, python2Packages, makeWrapper, unzip
+, guiSupport ? false, tk ? null
+, ApplicationServices
+, mercurialSrc ? fetchurl rec {
+    meta.name = "mercurial-${meta.version}";
+    meta.version = "4.9.1";
+    url = "https://mercurial-scm.org/release/${meta.name}.tar.gz";
+    sha256 = "0iybbkd9add066729zg01kwz5hhc1s6lhp9rrnsmzq6ihyxj3p8v";
+  }
+}:
+
+let
+  inherit (python2Packages) docutils hg-git dulwich python;
+
+in python2Packages.buildPythonApplication {
+
+  inherit (mercurialSrc.meta) name version;
+  src = mercurialSrc;
+
+  format = "other";
+
+  inherit python; # pass it so that the same version can be used in hg2git
+
+  buildInputs = [ makeWrapper docutils unzip ]
+    ++ stdenv.lib.optionals stdenv.isDarwin [ ApplicationServices ];
+
+  propagatedBuildInputs = [ hg-git dulwich ];
+
+  makeFlags = [ "PREFIX=$(out)" ];
+
+  postInstall = (stdenv.lib.optionalString guiSupport
+    ''
+      mkdir -p $out/etc/mercurial
+      cp contrib/hgk $out/bin
+      cat >> $out/etc/mercurial/hgrc << EOF
+      [extensions]
+      hgk=$out/lib/${python.libPrefix}/site-packages/hgext/hgk.py
+      EOF
+      # setting HG so that hgk can be run itself as well (not only hg view)
+      WRAP_TK=" --set TK_LIBRARY ${tk}/lib/${tk.libPrefix}
+                --set HG $out/bin/hg
+                --prefix PATH : ${tk}/bin "
+    '') +
+    ''
+      for i in $(cd $out/bin && ls); do
+        wrapProgram $out/bin/$i \
+          $WRAP_TK
+      done
+
+      # copy hgweb.cgi to allow use in apache
+      mkdir -p $out/share/cgi-bin
+      cp -v hgweb.cgi contrib/hgweb.wsgi $out/share/cgi-bin
+      chmod u+x $out/share/cgi-bin/hgweb.cgi
+
+      # install bash/zsh completions
+      install -v -m644 -D contrib/bash_completion $out/share/bash-completion/completions/_hg
+      install -v -m644 -D contrib/zsh_completion $out/share/zsh/site-functions/_hg
+    '';
+
+  meta = {
+    inherit (mercurialSrc.meta) version;
+    description = "A fast, lightweight SCM system for very large distributed projects";
+    homepage = https://www.mercurial-scm.org;
+    downloadPage = https://www.mercurial-scm.org/release/;
+    license = stdenv.lib.licenses.gpl2;
+    maintainers = [ stdenv.lib.maintainers.eraserhd ];
+    updateWalker = true;
+    platforms = stdenv.lib.platforms.unix;
+  };
+}
+
diff --git a/pkgs/applications/virtualization/conmon/default.nix b/pkgs/applications/virtualization/conmon/default.nix
index 77f3d271b59..49d14d25bab 100644
--- a/pkgs/applications/virtualization/conmon/default.nix
+++ b/pkgs/applications/virtualization/conmon/default.nix
@@ -9,13 +9,13 @@
 stdenv.mkDerivation rec {
   project = "conmon";
   name = "${project}-${version}";
-  version = "2.0.8";
+  version = "2.0.9";
 
   src = fetchFromGitHub {
     owner = "containers";
     repo = project;
     rev = "v${version}";
-    sha256 = "17pv80ba79wh4nwxy3wl0vl1m8054s346hgcp87iy3mpnrvq2cv2";
+    sha256 = "0wy3nihif9ih62rlskrjysshfaxdl878fj5ni1zfb9db4nsx6z0m";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/applications/virtualization/podman/default.nix b/pkgs/applications/virtualization/podman/default.nix
index fe7640be1c8..607d790247f 100644
--- a/pkgs/applications/virtualization/podman/default.nix
+++ b/pkgs/applications/virtualization/podman/default.nix
@@ -5,13 +5,13 @@
 
 buildGoPackage rec {
   pname = "podman";
-  version = "1.6.3";
+  version = "1.7.0";
 
   src = fetchFromGitHub {
     owner  = "containers";
     repo   = "libpod";
     rev    = "v${version}";
-    sha256 = "0y87pylpff2xl796n5s2vrm90pspzqfw8h4a5gndn1mx18s09s69";
+    sha256 = "1f1dq9g08mlm9y9d7jbs780nrfc25ln97ca5qifcsyc9bmp4f6r1";
   };
 
   goPackagePath = "github.com/containers/libpod";
diff --git a/pkgs/applications/window-managers/cwm/default.nix b/pkgs/applications/window-managers/cwm/default.nix
index c109cd5cb68..53489eca3a0 100644
--- a/pkgs/applications/window-managers/cwm/default.nix
+++ b/pkgs/applications/window-managers/cwm/default.nix
@@ -3,13 +3,13 @@
 stdenv.mkDerivation rec {
 
   pname = "cwm";
-  version = "6.3";
+  version = "6.6";
 
   src = fetchFromGitHub {
     owner = "leahneukirchen";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1m08gd6nscwfx6040zbg2zl89m4g73im68iflzcihd6pdc8rzzs4";
+    sha256 = "1rvb4y37vw3bpkqa6fbizgc74x3nrlkk6yf5hlm0hf8qz0c17vbl";
   };
 
   nativeBuildInputs = [ pkgconfig ];