NixOS · Oct 22, 2019 · Oct 23, 2019 · Oct 24, 2019 · Oct 24, 2019 · Oct 24, 2019
diff --git a/pkgs/applications/audio/strawberry/default.nix b/pkgs/applications/audio/strawberry/default.nix
@@ -35,13 +35,13 @@
 
 mkDerivation rec {
   pname = "strawberry";
-  version = "0.6.3";
+  version = "0.6.5";
 
   src = fetchFromGitHub {
     owner = "jonaski";
     repo = pname;
     rev = version;
-    sha256 = "01j5jzzicy895kg9sjy46lbcm5kvf3642d3q5wwb2fyvyq1fbcv0";
+    sha256 = "1kqx0q99n1p5pm6skvqjihz11byhxdid1qw6gqp67dh2na62z1lm";
   };
 
   buildInputs = [
@@ -89,9 +89,11 @@ mkDerivation rec {
 
   meta = with lib; {
     description = "Music player and music collection organizer";
-    license = licenses.gpl2;
+    homepage = "https://www.strawberrymusicplayer.org/";
+    changelog = "https://raw.githubusercontent.com/jonaski/strawberry/${version}/Changelog";
+    license = licenses.gpl3;
     maintainers = with maintainers; [ peterhoeg ];
-    # upstream says darwin should work but they lack maintainers as of 0.6.3
+    # upstream says darwin should work but they lack maintainers as of 0.6.5
     platforms = platforms.linux;
   };
 }
diff --git a/pkgs/applications/editors/emacs-modes/recipes-archive-melpa.json b/pkgs/applications/editors/emacs-modes/recipes-archive-melpa.json
diff --git a/pkgs/applications/graphics/yed/default.nix b/pkgs/applications/graphics/yed/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "yEd";
-  version = "3.19";
+  version = "3.19.1";
 
   src = fetchzip {
     url = "https://www.yworks.com/resources/yed/demo/${pname}-${version}.zip";
-    sha256 = "0l70pc7wl2ghfkjab9w2mbx7crwha7xwkrpmspsi5c6q56dw7s33";
+    sha256 = "19bnzpwszfrlpi5ssgfsv29gdmfj7pvxad9z8fdjf9k61187dgqj";
   };
 
   nativeBuildInputs = [ makeWrapper unzip ];

diff --git a/pkgs/applications/misc/xmrig/default.nix b/pkgs/applications/misc/xmrig/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "xmrig";
-  version = "3.1.3";
+  version = "3.2.0";
 
   src = fetchFromGitHub {
     owner = "xmrig";
     repo = "xmrig";
     rev = "v${version}";
-    sha256 = "05z3hpz42609zsrqwd9sbxkgzm4f28ajhvgk69jvcfw7azg5jcfq";
+    sha256 = "1qb20v3wvd6scx0dnlcqvj947ng4h0lxlvl9kpz0a2a3l5425rjf";
   };
 
   nativeBuildInputs = [ cmake ];

diff --git a/pkgs/applications/networking/cluster/nomad/default.nix b/pkgs/applications/networking/cluster/nomad/default.nix
@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   pname = "nomad";
-  version = "0.9.5";
+  version = "0.10.0";
   rev = "v${version}";
 
   goPackagePath = "github.com/hashicorp/nomad";
@@ -12,7 +12,7 @@ buildGoPackage rec {
     owner = "hashicorp";
     repo = pname;
     inherit rev;
-    sha256 = "01491470idb11z0ab4anb5caw46vy9s94a17l92j0z2f3f4k6xfl";
+    sha256 = "1hvnrbna4hsyp5byx5si2gn4h3m6shwmd8nk0vpbrs3ck3dl1p6l";
   };
 
   # ui:
@@ -36,6 +36,6 @@ buildGoPackage rec {
     description = "A Distributed, Highly Available, Datacenter-Aware Scheduler";
     platforms = platforms.unix;
     license = licenses.mpl20;
-    maintainers = with maintainers; [ rushmorem pradeepchhetri ];
+    maintainers = with maintainers; [ rushmorem pradeepchhetri endocrimes ];
   };
 }
diff --git a/pkgs/applications/networking/p2p/tixati/default.nix b/pkgs/applications/networking/p2p/tixati/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "tixati";
-  version = "2.62";
+  version = "2.64";
 
   src = fetchurl {
     url = "https://download2.tixati.com/download/tixati-${version}-1.x86_64.manualinstall.tar.gz";
-    sha256 = "18lmzllkymdigfl1xf696zqmr2b83p4rzlc8ddrcr0zpzy2z2w4a";
+    sha256 = "0xz2b2vasfc39wqv9lak2wdli7pr5b1vcm1lgpqx6kz7j5ba6jqp";
   };
 
   installPhase = ''

diff --git a/pkgs/applications/science/biology/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix
@@ -0,0 +1,43 @@
+{ lib
+, fetchFromGitHub
+, python3Packages
+}:
+
+python3Packages.buildPythonApplication rec {
+  pname = "truvari";
+  version = "1.3.2";
+
+  src = fetchFromGitHub {
+    owner = "spiralgenetics";
+    repo = "truvari";
+    rev = "v${version}";
+    sha256 = "0wmjz8nzibvj0ixky1m0qi7iyd204prk7glbvig1cvaab33k19f1";
+  };
+
+  propagatedBuildInputs = with python3Packages; [
+    pyvcf
+    python-Levenshtein
+    progressbar2
+    pysam
+    pyfaidx
+    intervaltree
+  ];
+
+  prePatch = ''
+    substituteInPlace ./setup.py \
+      --replace '"progressbar2==3.41.0",' "" \
+      --replace '"pysam==0.15.2",' ""
+  '';
+
+  meta = with lib; {
+    description = "Structural variant comparison tool for VCFs";
+    license = licenses.mit;
+    maintainers = with maintainers; [ scalavision ];
+    longDescription = ''
+      Truvari is a benchmarking tool for comparison sets of SVs.
+      It can calculate the recall, precision, and f-measure of a
+      vcf from a given structural variant caller. The tool
+      is created by Spiral Genetics.
+    '';
+  };
+}
diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "verilator";
-  version = "4.018";
+  version = "4.020";
 
   src = fetchurl {
     url    = "https://www.veripool.org/ftp/${pname}-${version}.tgz";
-    sha256 = "0ih38dd8hiwgjyc6gclx8i9jlycgdlrxzz8bicm4a6yj4p0jxmcq";
+    sha256 = "06n3vds762vza4byrav0j3kp3aivvadndkgw7nirvasclp19zmxb";
   };
 
   enableParallelBuilding = true;

diff --git a/pkgs/development/haskell-modules/configuration-common.nix b/pkgs/development/haskell-modules/configuration-common.nix
@@ -1048,7 +1048,7 @@ self: super: {
     generateOptparseApplicativeCompletion "dhall" (
       dontCheck super.dhall
   );
-  dhall_1_26_1 = dontCheck super.dhall_1_26_1;
+  dhall_1_27_0 = dontCheck super.dhall_1_27_0;
 
 
   # Missing test files in source distribution, fixed once 1.4.0 is bumped
@@ -1202,8 +1202,8 @@ self: super: {
   temporary-resourcet = doJailbreak super.temporary-resourcet;
 
   # Requires dhall >= 1.23.0
-  ats-pkg = super.ats-pkg.override { dhall = self.dhall_1_26_1; };
-  dhall-to-cabal = super.dhall-to-cabal.override { dhall = self.dhall_1_26_1; };
+  ats-pkg = super.ats-pkg.override { dhall = self.dhall_1_27_0; };
+  dhall-to-cabal = super.dhall-to-cabal.override { dhall = self.dhall_1_27_0; };
 
   # Test suite doesn't work with current QuickCheck
   # https://github.com/pruvisto/heap/issues/11
@@ -1269,4 +1269,11 @@ self: super: {
     });
   });
 
+  # upstream issue: https://github.com/vmchale/atspkg/issues/12
+  language-ats = dontCheck super.language-ats;
+
+  # polysemy has occasional test failures from what looks like buggy async tests.
+  # We think this will probably be fixed when updating to the polysemy version in LTS-15.
+  polysemy = dontCheck super.polysemy;
+
 } // import ./configuration-tensorflow.nix {inherit pkgs haskellLib;} self super
diff --git a/pkgs/development/haskell-modules/configuration-hackage2nix.yaml b/pkgs/development/haskell-modules/configuration-hackage2nix.yaml
@@ -43,14 +43,14 @@ core-packages:
   - ghcjs-base-0
 
 default-package-overrides:
-  # LTS Haskell 14.10
+  # LTS Haskell 14.11
   - abstract-deque ==0.3
   - abstract-deque-tests ==0.3
   - abstract-par ==0.3.3
   - accuerr ==0.2.0.2
   - ace ==0.6
   - action-permutations ==0.0.0.1
-  - active ==0.2.0.13
+  - active ==0.2.0.14
   - ad ==4.3.6
   - adjunctions ==4.4
   - adler32 ==0.1.2.0
@@ -73,7 +73,7 @@ default-package-overrides:
   - alarmclock ==0.7.0.2
   - alerts ==0.1.2.0
   - alex ==3.2.4
-  - alg ==0.2.11.0
+  - alg ==0.2.12.0
   - algebraic-graphs ==0.4
   - Allure ==0.9.5.0
   - almost-fix ==0.0.2
@@ -283,7 +283,7 @@ default-package-overrides:
   - cassava-records ==0.1.0.4
   - cast ==0.1.0.2
   - caster ==0.0.3.0
-  - category ==0.2.4.1
+  - category ==0.2.4.2
   - cayley-client ==0.4.9
   - cborg ==0.2.2.0
   - cborg-json ==0.2.1.0
@@ -399,7 +399,6 @@ default-package-overrides:
   - convertible ==1.1.1.0
   - cookie ==0.4.4
   - core-data ==0.2.0.0
-  - core-program ==0.2.0.0
   - core-text ==0.2.0.0
   - countable ==1.0
   - country ==0.1.6
@@ -521,7 +520,7 @@ default-package-overrides:
   - dhall-json ==1.3.0
   - diagrams ==1.4
   - diagrams-contrib ==1.4.3
-  - diagrams-core ==1.4.1.1
+  - diagrams-core ==1.4.2
   - diagrams-lib ==1.4.2.3
   - diagrams-postscript ==1.4.1
   - diagrams-rasterific ==1.4.1.1
@@ -563,7 +562,8 @@ default-package-overrides:
   - download ==0.3.2.7
   - drinkery ==0.4
   - dsp ==0.2.5
-  - dual-tree ==0.2.2
+  - dual ==0.1.0.2
+  - dual-tree ==0.2.2.1
   - dublincore-xml-conduit ==0.1.0.2
   - dunai ==0.5.1
   - dunai-core ==0.5.1.0
@@ -915,7 +915,7 @@ default-package-overrides:
   - hinfo ==0.0.3.0
   - hinotify ==0.4
   - hint ==0.9.0.2
-  - hjsmin ==0.2.0.3
+  - hjsmin ==0.2.0.4
   - hkgr ==0.2.4
   - hlibgit2 ==0.18.0.16
   - hlibsass ==0.1.8.0
@@ -980,7 +980,7 @@ default-package-overrides:
   - hspec-discover ==2.7.1
   - hspec-expectations ==0.8.2
   - hspec-expectations-lifted ==0.10.0
-  - hspec-expectations-pretty-diff ==0.7.2.4
+  - hspec-expectations-pretty-diff ==0.7.2.5
   - hspec-golden-aeson ==0.7.0.0
   - hspec-leancheck ==0.0.3
   - hspec-megaparsec ==2.0.1
@@ -1179,7 +1179,7 @@ default-package-overrides:
   - LambdaHack ==0.9.5.0
   - lame ==0.2.0
   - language-c ==0.8.3
-  - language-c-quote ==0.12.2
+  - language-c-quote ==0.12.2.1
   - language-docker ==8.0.2
   - language-ecmascript ==0.19
   - language-haskell-extract ==0.2.4
@@ -1370,7 +1370,7 @@ default-package-overrides:
   - monad-unlift-ref ==0.2.1
   - mongoDB ==2.5.0.0
   - monoidal-containers ==0.4.0.0
-  - monoid-extras ==0.5
+  - monoid-extras ==0.5.1
   - monoid-subclasses ==0.4.6.1
   - monoid-transformer ==0.0.4
   - mono-traversable ==1.0.13.0
@@ -1403,7 +1403,7 @@ default-package-overrides:
   - mysql-simple ==0.4.5
   - n2o ==0.11.1
   - nagios-check ==0.3.2
-  - named ==0.3.0.0
+  - named ==0.3.0.1
   - names-th ==0.3.0.0
   - nano-erl ==0.1.0.1
   - nanospec ==0.2.2
@@ -1472,7 +1472,7 @@ default-package-overrides:
   - odbc ==0.2.2
   - oeis ==0.3.9
   - oeis2 ==1.0.3
-  - ofx ==0.4.2.0
+  - ofx ==0.4.4.0
   - old-locale ==1.0.0.7
   - old-time ==1.1.0.3
   - once ==0.4
@@ -1716,13 +1716,13 @@ default-package-overrides:
   - Ranged-sets ==0.4.0
   - range-set-list ==0.1.3.1
   - rank1dynamic ==0.4.0
-  - rank2classes ==1.3.1.1
+  - rank2classes ==1.3.1.2
   - Rasterific ==0.7.4.4
   - rasterific-svg ==0.3.3.2
   - ratel ==1.0.8
   - ratel-wai ==1.1.0
   - rattle ==0.1
-  - rattletrap ==9.0.2
+  - rattletrap ==9.0.6
   - rawfilepath ==0.2.4
   - rawstring-qm ==0.2.3.0
   - raw-strings-qq ==1.1
@@ -1769,6 +1769,8 @@ default-package-overrides:
   - repa ==3.4.1.4
   - repa-algorithms ==3.4.1.3
   - repa-io ==3.4.1.1
+  - replace-attoparsec ==1.0.2.0
+  - replace-megaparsec ==1.1.4.0
   - repline ==0.2.1.0
   - req ==2.1.0
   - req-conduit ==1.0.0
@@ -1881,6 +1883,7 @@ default-package-overrides:
   - servant-mock ==0.8.5
   - servant-multipart ==0.11.4
   - servant-pipes ==0.15.1
+  - servant-rawm ==0.3.2.0
   - servant-ruby ==0.9.0.0
   - servant-server ==0.16.2
   - servant-static-th ==0.2.2.1
@@ -1996,7 +1999,7 @@ default-package-overrides:
   - storable-tuple ==0.0.3.3
   - storablevector ==0.2.13
   - store ==0.5.1.2
-  - store-core ==0.4.4
+  - store-core ==0.4.4.1
   - Strafunski-StrategyLib ==5.0.1.0
   - stratosphere ==0.40.0
   - streaming ==0.2.3.0
@@ -2143,7 +2146,7 @@ default-package-overrides:
   - throwable-exceptions ==0.1.0.9
   - th-strict-compat ==0.1.0.1
   - th-test-utils ==1.0.1
-  - th-utilities ==0.2.3.0
+  - th-utilities ==0.2.3.1
   - thyme ==0.3.5.5
   - tile ==0.3.0.0
   - time-compat ==1.9.2.2
@@ -2225,7 +2228,7 @@ default-package-overrides:
   - ucam-webauth ==0.1.0.0
   - ucam-webauth-types ==0.1.0.0
   - uglymemo ==0.1.0.1
-  - unagi-chan ==0.4.1.2
+  - unagi-chan ==0.4.1.3
   - unbounded-delays ==0.1.1.0
   - unbound-generics ==0.4.0
   - unboxed-ref ==0.4.0.0
@@ -2275,7 +2278,7 @@ default-package-overrides:
   - users-test ==0.5.0.1
   - utf8-light ==0.4.2
   - utf8-string ==1.0.1.1
-  - util ==0.1.13.0
+  - util ==0.1.14.0
   - utility-ht ==0.0.14
   - uuid ==1.3.13
   - uuid-types ==1.0.3
@@ -2309,7 +2312,7 @@ default-package-overrides:
   - verbosity ==0.3.0.0
   - versions ==3.5.1.1
   - ViennaRNAParser ==1.3.3
-  - viewprof ==0.0.0.31
+  - viewprof ==0.0.0.32
   - vinyl ==0.11.0
   - vivid ==0.4.2.3
   - vivid-osc ==0.5.0.0
@@ -2818,6 +2821,7 @@ broken-packages:
   - aeson-tiled
   - aeson-typescript
   - affection
+  - affine
   - affine-invariant-ensemble-mcmc
   - afv
   - ag-pictgen
@@ -2827,6 +2831,7 @@ broken-packages:
   - agda-snippets-hakyll
   - agentx
   - AGI
+  - agum
   - AhoCorasick
   - aig
   - aip
@@ -2841,6 +2846,7 @@ broken-packages:
   - alex-meta
   - alex-prelude
   - alfred
+  - alg
   - alga
   - algebra
   - algebra-sql
@@ -2953,6 +2959,7 @@ broken-packages:
   - ApproxFun-hs
   - arb-fft
   - arbb-vm
+  - arbor-monad-counter
   - arbor-monad-logger
   - arbor-monad-metric
   - arbor-monad-metric-datadog
@@ -3172,6 +3179,7 @@ broken-packages:
   - bidirectionalization-combined
   - bidispec
   - bidispec-extras
+  - bifunctor
   - BiGUL
   - billboard-parser
   - billeksah-forms
@@ -3412,6 +3420,7 @@ broken-packages:
   - c0parser
   - c2ats
   - c2hsc
+  - ca
   - cabal-audit
   - cabal-bundle-clib
   - cabal-cache
@@ -3522,6 +3531,7 @@ broken-packages:
   - Catana
   - catch-fd
   - categorical-algebra
+  - category
   - category-extras
   - category-traced
   - catnplus
@@ -3685,6 +3695,7 @@ broken-packages:
   - cmonad
   - cmph
   - cmt
+  - cmu
   - cmv
   - cnc-spec-compiler
   - co-log
@@ -3814,7 +3825,9 @@ broken-packages:
   - constrained-category
   - constrained-dynamic
   - constrained-monads
+  - constraint
   - constraint-manip
+  - constraint-reflection
   - ConstraintKinds
   - constraints-emerge
   - constructive-algebra
@@ -3859,6 +3872,7 @@ broken-packages:
   - COrdering
   - core
   - core-haskell
+  - core-program
   - corebot-bliki
   - CoreDump
   - CoreErlang
@@ -3933,6 +3947,7 @@ broken-packages:
   - cryptocompare
   - cryptoconditions
   - cryptol
+  - cryptostore
   - cryptsy-api
   - crystalfontz
   - csa
@@ -5108,7 +5123,6 @@ broken-packages:
   - grakn
   - grammar-combinators
   - GrammarProducts
-  - grammatical-parsers
   - grapefruit-examples
   - grapefruit-frp
   - grapefruit-records
@@ -6416,6 +6430,7 @@ broken-packages:
   - iteratee-stm
   - iterIO
   - iterio-server
+  - ival
   - ivor
   - ivory
   - ivory-backend-c
@@ -7179,6 +7194,8 @@ broken-packages:
   - mlist
   - mltool
   - mm2
+  - mmsyn2
+  - mmsyn4
   - mmtf
   - mmtl
   - mmtl-base
@@ -8015,6 +8032,7 @@ broken-packages:
   - precursor
   - pred-trie
   - predicate-class
+  - predicate-typed
   - prednote
   - prednote-test
   - prefork
@@ -8061,6 +8079,7 @@ broken-packages:
   - procrastinating-variable
   - procstat
   - producer
+  - product
   - prof2dot
   - prof2pretty
   - progress
@@ -8247,6 +8266,7 @@ broken-packages:
   - rasa-ext-vim
   - rascal
   - Rasenschach
+  - rational-list
   - rattle
   - rattletrap
   - raven-haskell-scotty
@@ -8277,6 +8297,7 @@ broken-packages:
   - read-io
   - reader-soup
   - readline-statevar
+  - readme-lhs
   - readpyc
   - readshp
   - really-simple-xml-parser
@@ -8654,6 +8675,8 @@ broken-packages:
   - Semantique
   - semdoc
   - semi-iso
+  - semialign-indexed
+  - semialign-optics
   - semibounded-lattices
   - Semigroup
   - semigroupoids-syntax
@@ -9015,6 +9038,7 @@ broken-packages:
   - SourceGraph
   - sousit
   - soyuz
+  - spacecookie
   - SpaceInvaders
   - spacepart
   - SpacePrivateers
@@ -9255,6 +9279,7 @@ broken-packages:
   - swearjure
   - swf
   - swift-lda
+  - sws
   - syb-extras
   - syb-with-class-instances-text
   - SybWidget
@@ -9725,6 +9750,7 @@ broken-packages:
   - unagi-bloomfilter
   - unagi-streams
   - unamb-custom
+  - unbeliever
   - unbound
   - unbound-kind-generics
   - unbounded-delays-units

diff --git a/pkgs/development/haskell-modules/hackage-packages.nix b/pkgs/development/haskell-modules/hackage-packages.nix
diff --git a/pkgs/development/libraries/spdlog/default.nix b/pkgs/development/libraries/spdlog/default.nix
@@ -3,7 +3,7 @@
 let
   generic = { version, sha256 }:
     stdenv.mkDerivation {
-      name = "spdlog-${version}";
+      pname = "spdlog";
       inherit version;
 
       src = fetchFromGitHub {
@@ -15,7 +15,7 @@ let
 
       nativeBuildInputs = [ cmake ];
 
-      cmakeFlags = [ "-DSPDLOG_BUILD_EXAMPLES=OFF" "-DSPDLOG_BUILD_BENCH=OFF" ];
+      cmakeFlags = [ "-DSPDLOG_BUILD_EXAMPLE=OFF" "-DSPDLOG_BUILD_BENCH=OFF" ];
 
       outputs = [ "out" "doc" ];
 
@@ -25,8 +25,8 @@ let
       '';
 
       meta = with stdenv.lib; {
-        description    = "Very fast, header only, C++ logging library.";
-        homepage       = https://github.com/gabime/spdlog;
+        description    = "Very fast, header only, C++ logging library";
+        homepage       = "https://github.com/gabime/spdlog";
         license        = licenses.mit;
         maintainers    = with maintainers; [ obadz ];
         platforms      = platforms.all;
@@ -35,8 +35,8 @@ let
 in
 {
   spdlog_1 = generic {
-    version = "1.3.1";
-    sha256 = "1rd4zmrlkcdjx0m0wpmjm1g9srj7jak6ai08qkhbn2lsn0niifzd";
+    version = "1.4.2";
+    sha256 = "1qc3rphvik44136ms0gjq2wmkl6qglri4fqxlhr2l5jwm8zhr8fc";
   };
 
   spdlog_0 = generic {

diff --git a/pkgs/development/python-modules/pyvcf/default.nix b/pkgs/development/python-modules/pyvcf/default.nix
@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "PyVCF";
+  version = "0.6.8";
+
+  src = fetchFromGitHub {
+    owner = "jamescasbon";
+    repo = "PyVCF";
+    rev = "476169cd457ba0caa6b998b301a4d91e975251d9";
+    sha256 = "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p";
+  };
+
+  checkInputs = [ pytest ];
+
+  meta = with lib; {
+    homepage = "https://pyvcf.readthedocs.io/en/latest/index.html";
+    description = "A VCF (Variant Call Format) Parser for Python, supporting version 4.0 and 4.1";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ scalavision ];
+    longDescription = ''
+      The intent of this module is to mimic the csv module in the Python stdlib, 
+      as opposed to more flexible serialization formats like JSON or YAML. 
+      vcf will attempt to parse the content of each record based on the data 
+      types specified in the meta-information lines
+    '';
+  };
+}
diff --git a/pkgs/development/tools/build-managers/bazel/default.nix b/pkgs/development/tools/build-managers/bazel/default.nix
@@ -22,11 +22,11 @@
 }:
 
 let
-  version = "1.0.0";
+  version = "1.1.0";
 
   src = fetchurl {
     url = "https://github.com/bazelbuild/bazel/releases/download/${version}/bazel-${version}-dist.zip";
-    sha256 = "1b4c9wav5zsldlwzsb064z3m5l4ns8i90bsvd5f215fxd45sy7f6";
+    sha256 = "1awm5wa4y4c37zy7d1ass83amwq5992wydkj5v9jx0zp7b4shrjb";
   };
 
   # Update with `eval $(nix-build -A bazel.updater)`,
@@ -46,11 +46,11 @@ let
       srcs.io_bazel_rules_sass
       srcs.platforms
       (if stdenv.hostPlatform.isDarwin
-       then srcs."java_tools_javac11_darwin-v5.1.zip"
-       else srcs."java_tools_javac11_linux-v5.1.zip")
+       then srcs."java_tools_javac11_darwin-v6.1.zip"
+       else srcs."java_tools_javac11_linux-v6.1.zip")
       srcs."coverage_output_generator-v2.0.zip"
       srcs.build_bazel_rules_nodejs
-      srcs."android_tools_pkg-0.10.tar.gz"
+      srcs."android_tools_pkg-0.11.tar.gz"
       srcs."0.28.3.tar.gz"
       srcs.rules_pkg
       srcs.rules_cc
@@ -107,7 +107,7 @@ let
   remote_java_tools = stdenv.mkDerivation {
     name = "remote_java_tools_${system}";
 
-    src = srcDepsSet."java_tools_javac11_${system}-v5.1.zip";
+    src = srcDepsSet."java_tools_javac11_${system}-v6.1.zip";
 
     nativeBuildInputs = [ autoPatchelfHook unzip ];
     buildInputs = [ gcc-unwrapped ];
@@ -222,8 +222,10 @@ stdenv.mkDerivation rec {
         sha256 = "03c1bwlq5bs3hg96v4g4pg2vqwhqq6w538h66rcpw02f83yy7fs8";
       };
 
-    in {
+    in (if !stdenv.hostPlatform.isDarwin then {
+      # `extracted` doesn’t work on darwin
       shebang = callPackage ./shebang-test.nix { inherit runLocal extracted bazelTest distDir; };
+    } else {}) // {
       bashTools = callPackage ./bash-tools-test.nix { inherit runLocal bazelTest distDir; };
       cpp = callPackage ./cpp-test.nix { inherit runLocal bazelTest bazel-examples distDir; };
       java = callPackage ./java-test.nix { inherit runLocal bazelTest bazel-examples distDir; };

diff --git a/pkgs/development/tools/build-managers/bazel/src-deps.json b/pkgs/development/tools/build-managers/bazel/src-deps.json
@@ -55,11 +55,11 @@
             "https://github.com/bazelbuild/rules_proto/archive/97d8af4dc474595af3900dd85cb3a29ad28cc313.tar.gz"
         ]
     },
-    "android_tools_pkg-0.10.tar.gz": {
-        "name": "android_tools_pkg-0.10.tar.gz",
-        "sha256": "9c5081f93276fefb3db7ca61cc1225ff6d1913e7e315568265bb1a728265a9b1",
+    "android_tools_pkg-0.11.tar.gz": {
+        "name": "android_tools_pkg-0.11.tar.gz",
+        "sha256": "6fc50151063bffdda700038ea7df99c89d54dc066e9377a5baff60d55d482ad2",
         "urls": [
-            "https://mirror.bazel.build/bazel_android_tools/android_tools_pkg-0.10.tar.gz"
+            "https://mirror.bazel.build/bazel_android_tools/android_tools_pkg-0.11.tar.gz"
         ]
     },
     "bazel_j2objc": {
@@ -165,25 +165,25 @@
             "https://github.com/bazelbuild/skydoc/archive/c7bbde2950769aac9a99364b0926230060a3ce04.tar.gz"
         ]
     },
-    "java_tools_javac11_darwin-v5.1.zip": {
-        "name": "java_tools_javac11_darwin-v5.1.zip",
-        "sha256": "2fa01b4cb69e33f85a96ba0620a2e6261f789eefdbeaeb1d2879140b50108db7",
+    "java_tools_javac11_darwin-v6.1.zip": {
+        "name": "java_tools_javac11_darwin-v6.1.zip",
+        "sha256": "f0c488dac18f18ab1a0d18bbd65288c7a128e90a24d9c16f65bd8243f79483a0",
         "urls": [
-            "https://mirror.bazel.build/bazel_java_tools/releases/javac11/v5.1/java_tools_javac11_darwin-v5.1.zip"
+            "https://mirror.bazel.build/bazel_java_tools/releases/javac11/v6.1/java_tools_javac11_darwin-v6.1.zip"
         ]
     },
-    "java_tools_javac11_linux-v5.1.zip": {
-        "name": "java_tools_javac11_linux-v5.1.zip",
-        "sha256": "ea2ee2f9eab37e04eae5aa8a266373132fe57676c25ea033504bc5438d6bc1ba",
+    "java_tools_javac11_linux-v6.1.zip": {
+        "name": "java_tools_javac11_linux-v6.1.zip",
+        "sha256": "12f7940ed0bc4c2e82238951cdf19b4179c7dcc361d16fe40fe4266538fb4ac6",
         "urls": [
-            "https://mirror.bazel.build/bazel_java_tools/releases/javac11/v5.1/java_tools_javac11_linux-v5.1.zip"
+            "https://mirror.bazel.build/bazel_java_tools/releases/javac11/v6.1/java_tools_javac11_linux-v6.1.zip"
         ]
     },
-    "java_tools_javac11_windows-v5.1.zip": {
-        "name": "java_tools_javac11_windows-v5.1.zip",
-        "sha256": "b2cfebc049c349268a7ca0e5ff37160899f87f6fe6a80a789de3df90db4ce4ef",
+    "java_tools_javac11_windows-v6.1.zip": {
+        "name": "java_tools_javac11_windows-v6.1.zip",
+        "sha256": "e2deb2efff684de78787e0bdc7620f9672d13f04a12856d8e7f677369a8e286b",
         "urls": [
-            "https://mirror.bazel.build/bazel_java_tools/releases/javac11/v5.1/java_tools_javac11_windows-v5.1.zip"
+            "https://mirror.bazel.build/bazel_java_tools/releases/javac11/v6.1/java_tools_javac11_windows-v6.1.zip"
         ]
     },
     "java_tools_langtools_javac10": {

diff --git a/pkgs/development/tools/misc/sccache/default.nix b/pkgs/development/tools/misc/sccache/default.nix
@@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, cargo, rustc, rustPlatform, pkgconfig, glib, openssl, darwin }:
 
 rustPlatform.buildRustPackage rec {
-  version = "0.2.11";
+  version = "0.2.12";
   pname = "sccache";
 
   src = fetchFromGitHub {
     owner = "mozilla";
     repo = "sccache";
     rev = version;
-    sha256 = "0084ddvzjgdpkwqc38kvzaz8n6av9ml3qqlkjma70hsis8w8gqjz";
+    sha256 = "1yd3rfp032crwlmfn2p3z12f67q7bxm78fhvdlc7azm2a4hkif4k";
   };
   cargoSha256 = "1bkglgrasyjyzjj9mwm32d3g3mg5yv74jj3zl7jf20dlq3rg3fh6";
 

diff --git a/pkgs/os-specific/linux/v4l2loopback/default.nix b/pkgs/os-specific/linux/v4l2loopback/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "v4l2loopback-${version}-${kernel.version}";
-  version = "0.12.0";
+  version = "0.12.2";
 
   src = fetchFromGitHub {
     owner = "umlaeute";
     repo = "v4l2loopback";
     rev = "v${version}";
-    sha256 = "1rf8dvabksxb2sj14j32h7n7pw7byqfnpqs4m4afj3398y9y23c4";
+    sha256 = "1bcypfz5nlfmdm2a00yl7rgl0jh0g2nmwndxlsrblqclznhjilg2";
   };
 
   hardeningDisable = [ "format" "pic" ];

diff --git a/pkgs/shells/zsh/oh-my-zsh/default.nix b/pkgs/shells/zsh/oh-my-zsh/default.nix
@@ -4,13 +4,13 @@
 { stdenv, fetchgit }:
 
 stdenv.mkDerivation rec {
-  version = "2019-10-22";
+  version = "2019-10-24";
   pname = "oh-my-zsh";
-  rev = "40df67bc3b9b51caa24df5d220487043040d1f9a";
+  rev = "9d790ea60ce1d3af265dfc05b77d77bd94b801d7";
 
   src = fetchgit { inherit rev;
     url = "https://github.com/robbyrussell/oh-my-zsh";
-    sha256 = "0dlkfgnhlqymgr9289j15kpcig2k184j0md7bkxn7w8v7c02xbbc";
+    sha256 = "15zvfvi7zr2pvqpy22w2ahcy2nbx1mmv1wcx5wcsr2nffgq8nanc";
   };
 
   pathsToLink = [ "/share/oh-my-zsh" ];

diff --git a/pkgs/tools/misc/you-get/default.nix b/pkgs/tools/misc/you-get/default.nix
@@ -2,15 +2,15 @@
 
 buildPythonApplication rec {
   pname = "you-get";
-  version = "0.4.1347";
+  version = "0.4.1355";
 
   # Tests aren't packaged, but they all hit the real network so
   # probably aren't suitable for a build environment anyway.
   doCheck = false;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "11wqk0q2nim7mmi247sflk4sq4yac3f4s71a6kldhbb94l4p8q26";
+    sha256 = "06y9q336az8dzkxc13rzhl0m6l298saaida75wsd9fjm8pych6fx";
   };
 
   meta = with stdenv.lib; {

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
@@ -5093,7 +5093,9 @@ in
 
   noip = callPackage ../tools/networking/noip { };
 
-  nomad = callPackage ../applications/networking/cluster/nomad { };
+ nomad = callPackage ../applications/networking/cluster/nomad {
+    buildGoPackage = buildGo112Package;
+  };
 
   notable = callPackage ../applications/misc/notable { };
 
@@ -23280,6 +23282,8 @@ in
 
   trimal = callPackage ../applications/science/biology/trimal { };
 
+  truvari = callPackage ../applications/science/biology/truvari { };
+
   varscan = callPackage ../applications/science/biology/varscan { };
 
   hmmer = callPackage ../applications/science/biology/hmmer { };

diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
@@ -1167,6 +1167,8 @@ in {
 
   pyvcd = callPackage ../development/python-modules/pyvcd { };
 
+  pyvcf = callPackage ../development/python-modules/pyvcf { };
+
   pyvoro = callPackage ../development/python-modules/pyvoro { };
 
   relatorio = callPackage ../development/python-modules/relatorio { };