NixOS · Sep 24, 2020 · Sep 24, 2020 · Sep 24, 2020 · Sep 24, 2020 · Sep 24, 2020
diff --git a/nixos/modules/services/monitoring/datadog-agent.nix b/nixos/modules/services/monitoring/datadog-agent.nix
@@ -6,7 +6,7 @@ let
   cfg = config.services.datadog-agent;
 
   ddConf = {
-    dd_url              = "https://app.datadoghq.com";
+    dd_url              = cfg.ddUrl;
     skip_ssl_validation = false;
     confd_path          = "/etc/datadog-agent/conf.d";
     additional_checksd  = "/etc/datadog-agent/checks.d";
@@ -77,6 +77,18 @@ in {
       type = types.path;
     };
 
+    ddUrl = mkOption {
+      description = ''
+        Custom dd_url to configure the agent with.
+        Useful when you want to point datadog to another endpoint, either
+        because you need a proxy to send out data, or because you use their EU
+        endpoint.
+      '';
+      default = "https://app.datadoghq.com";
+      example = "https://app.datadoghq.eu";
+      type = types.str;
+    };
+
     tags = mkOption {
       description = "The tags to mark this Datadog agent";
       example = [ "test" "service" ];

diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix
@@ -11,8 +11,15 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ zlib ];
 
+  # it's unclear which headers are intended to be part of the public interface
+  # so we may find ourselves having to add more here over time
   installPhase = ''
-    install -vD bwa $out/bin/bwa
+    install -vD -t $out/bin bwa
+    install -vD -t $out/lib libbwa.a
+    install -vD -t $out/include bntseq.h
+    install -vD -t $out/include bwa.h
+    install -vD -t $out/include bwamem.h
+    install -vD -t $out/include bwt.h
   '';
 
   meta = with stdenv.lib; {

diff --git a/pkgs/applications/science/biology/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix
@@ -5,13 +5,13 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "truvari";
-  version = "1.3.4";
+  version = "2.0.2";
 
   src = fetchFromGitHub {
     owner = "spiralgenetics";
     repo = "truvari";
     rev = "v${version}";
-    sha256 = "1bph7v48s7pyfagz8a2fzl5fycjliqzn5lcbv3m2bp2ih1f1gd1v";
+    sha256 = "0lp1wnldjv92k4ncga1h0icb0dpjsrx427vggg40x04a7kp9lwx0";
   };
 
   propagatedBuildInputs = with python3Packages; [
@@ -21,17 +21,20 @@ python3Packages.buildPythonApplication rec {
     pysam
     pyfaidx
     intervaltree
+    pytabix
+    acebinf
+    bwapy
+    joblib
+    pandas
   ];
 
-  prePatch = ''
-    substituteInPlace ./setup.py \
-      --replace '"progressbar2==3.41.0",' '"progressbar2==3.47.0",' \
-      --replace '"pysam==0.15.2",' '"pysam==0.15.4",' \
-      --replace '"pyfaidx==0.5.5.2",' '"pyfaidx==0.5.8",'
-  '';
+  # no tests
+  doCheck = false;
+  pythonImportsCheck = [ "truvari" ];
 
   meta = with lib; {
     description = "Structural variant comparison tool for VCFs";
+    homepage = "https://github.com/spiralgenetics/truvari";
     license = licenses.mit;
     maintainers = with maintainers; [ scalavision ];
     longDescription = ''

diff --git a/pkgs/applications/science/logic/avy/0001-no-static-boost-libs.patch b/pkgs/applications/science/logic/avy/0001-no-static-boost-libs.patch
diff --git a/pkgs/applications/science/logic/avy/default.nix b/pkgs/applications/science/logic/avy/default.nix
@@ -1,13 +1,13 @@
 { stdenv, fetchgit, cmake, zlib, boost }:
 
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
   pname = "avy";
-  version = "2017.10.16";
+  version = "2019.05.01"; # date of cav19 tag
 
   src = fetchgit {
     url    = "https://bitbucket.org/arieg/extavy";
-    rev    = "c75c83379c38d6ea1046d0caee95aef77283ffe3";
-    sha256 = "0zcycnypg4q5g710bnkjpycaawmibc092vmyhgfbixkgq9fb5lfh";
+    rev    = "cav19";
+    sha256 = "0qdzy9srxp5f38x4dbb3prnr9il6cy0kz80avrvd7fxqzy7wdlwy";
     fetchSubmodules = true;
   };
 
@@ -31,10 +31,6 @@ stdenv.mkDerivation {
     patch -p1 -d glucose -i ${./glucose-fenv.patch}
   '';
 
-  patches =
-    [ ./0001-no-static-boost-libs.patch
-    ];
-
   installPhase = ''
     mkdir -p $out/bin
     cp avy/src/{avy,avybmc} $out/bin/

diff --git a/pkgs/development/python-modules/acebinf/default.nix b/pkgs/development/python-modules/acebinf/default.nix
@@ -0,0 +1,28 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pyvcf
+}:
+
+buildPythonPackage rec {
+  pname = "ACEBinf";
+  version = "1.0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1168pny671l6zfm2vv1pwspnflmzi7f4v8yldjl7zlz0b9cm5zlz";
+  };
+
+  buildInputs = [ pyvcf ];
+
+  # no tests
+  doCheck = false;
+  pythonImportsCheck = [ "acebinf" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/ACEnglish/acebinf";
+    description = "Collection of simple utilities used when building bioinformatics tools";
+    license = licenses.unlicense;
+    maintainers = with maintainers; [ ris ];
+  };
+}
diff --git a/pkgs/development/python-modules/bwapy/default.nix b/pkgs/development/python-modules/bwapy/default.nix
@@ -0,0 +1,42 @@
+{ stdenv
+, buildPythonPackage
+, pythonOlder
+, fetchPypi
+, bwa
+, cffi
+, zlib
+}:
+
+buildPythonPackage rec {
+  pname = "bwapy";
+  version = "0.1.4";
+  disabled = pythonOlder "3.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "090qwx3vl729zn3a7sksbviyg04kc71gpbm3nd8dalqp673x1npw";
+  };
+  postPatch = ''
+    # replace bundled bwa
+    rm -r bwa/*
+    cp ${bwa}/lib/*.a ${bwa}/include/*.h bwa/
+
+    substituteInPlace setup.py \
+      --replace 'setuptools>=49.2.0' 'setuptools'
+  '';
+
+  buildInputs = [ zlib bwa ];
+
+  propagatedBuildInputs = [ cffi ];
+
+  # no tests
+  doCheck = false;
+  pythonImportsCheck = [ "bwapy" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/ACEnglish/acebinf";
+    description = "Python bindings to bwa mem aligner";
+    license = licenses.mpl20;
+    maintainers = with maintainers; [ ris ];
+  };
+}
diff --git a/pkgs/development/python-modules/gssapi/default.nix b/pkgs/development/python-modules/gssapi/default.nix
@@ -1,14 +1,13 @@
 { stdenv
 , lib
 , buildPythonPackage
+, pythonOlder
 , fetchFromGitHub
 , six
-, enum34
 , decorator
 , nose
 , krb5Full
 , darwin
-, isPy27
 , parameterized
 , shouldbe
 , cython
@@ -18,13 +17,14 @@
 
 buildPythonPackage rec {
   pname = "gssapi";
-  version = "1.6.2";
+  version = "1.6.9";
+  disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "pythongssapi";
     repo = "python-${pname}";
     rev = "v${version}";
-    sha256 = "195x3zqzyv491i9hf7l4asmic5pb2w3l1r7bps89651wkb3mrz1l";
+    sha256 = "1shm3pc0l2r91qadkpq4bx45my0165nw3kdcp0gw4lk50z215hag";
   };
 
   # It's used to locate headers
@@ -41,7 +41,7 @@ buildPythonPackage rec {
   propagatedBuildInputs =  [
     decorator
     six
-  ] ++ lib.optional isPy27 enum34;
+  ];
 
   buildInputs = lib.optionals stdenv.isDarwin [
     darwin.apple_sdk.frameworks.GSS
@@ -55,12 +55,21 @@ buildPythonPackage rec {
     six
   ];
 
-  doCheck = !stdenv.isDarwin; # many failures on darwin
+  doCheck = pythonOlder "3.8"  # `shouldbe` not available
+    && !stdenv.isDarwin;  # many failures on darwin
 
+  # skip tests which fail possibly due to be an upstream issue (see
+  # https://github.com/pythongssapi/python-gssapi/issues/220)
   checkPhase = ''
+    # some tests don't respond to being disabled through nosetests -x
+    echo $'\ndel CredsTestCase.test_add_with_impersonate' >> gssapi/tests/test_high_level.py
+    echo $'\ndel TestBaseUtilities.test_acquire_creds_impersonate_name' >> gssapi/tests/test_raw.py
+    echo $'\ndel TestBaseUtilities.test_add_cred_impersonate_name' >> gssapi/tests/test_raw.py
+
     export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH"
-    ${python.interpreter} setup.py nosetests
+    ${python.interpreter} setup.py nosetests -e 'ext_test_\d.*'
   '';
+  pythonImportsCheck = [ "gssapi" ];
 
   meta = with lib; {
     homepage = "https://pypi.python.org/pypi/gssapi";

diff --git a/pkgs/development/python-modules/pamqp/default.nix b/pkgs/development/python-modules/pamqp/default.nix
@@ -9,12 +9,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "3.0.1";
+  version = "2.3.0";
   pname = "pamqp";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0a9b49bde3f554ec49b47ebdb789133979985f24d5f4698935ed589a2d4392a4";
+    sha256 = "1s4lwbsiikz3czqad7jarb7k303q0wamla0rirghvwl9bslgbl2w";
   };
 
   buildInputs = [ mock nose pep8 pylint mccabe ];

diff --git a/pkgs/development/python-modules/pytabix/default.nix b/pkgs/development/python-modules/pytabix/default.nix
@@ -0,0 +1,32 @@
+{ stdenv
+, buildPythonPackage
+, isPy3k
+, fetchPypi
+, zlib
+}:
+
+buildPythonPackage rec {
+  pname = "pytabix";
+  version = "0.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ldp5r4ggskji6qx4bp2qxy2vrvb3fam03ksn0gq2hdxgrlg2x07";
+  };
+
+  buildInputs = [ zlib ];
+
+  doCheck = !isPy3k;
+  preCheck = ''
+    substituteInPlace test/test.py \
+      --replace 'test_remote_file' 'dont_test_remote_file'
+  '';
+  pythonImportsCheck = [ "tabix" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/slowkow/pytabix";
+    description = "Python interface for tabix";
+    license = licenses.mit;
+    maintainers = with maintainers; [ ris ];
+  };
+}
diff --git a/pkgs/development/python-modules/rabbitpy/default.nix b/pkgs/development/python-modules/rabbitpy/default.nix
@@ -7,15 +7,15 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.0.0";
+  version = "2.0.1";
   pname = "rabbitpy";
 
   # No tests in the pypi tarball, so we directly fetch from git
   src = fetchFromGitHub {
     owner = "gmr";
     repo = pname;
     rev = version;
-    sha256 = "0fd80zlr4p2sh77rxyyfi9l0h2zqi2csgadr0rhnpgpqsy10qck6";
+    sha256 = "0m5z3i3d5adrz1wh6y35xjlls3cq6p4y9p1mzghw3k7hdvg26cck";
   };
 
   propagatedBuildInputs = [ pamqp ];
@@ -31,7 +31,7 @@ buildPythonPackage rec {
   postPatch = ''
     # See: https://github.com/gmr/rabbitpy/issues/118
     substituteInPlace setup.py \
-      --replace 'pamqp>=1.6.1,<2.0' 'pamqp'
+      --replace 'pamqp>=2,<3' 'pamqp'
   '';
 
   meta = with stdenv.lib; {

diff --git a/pkgs/os-specific/linux/kernel/hardened/patches.json b/pkgs/os-specific/linux/kernel/hardened/patches.json
@@ -10,18 +10,18 @@
         "url": "https://github.com/anthraxx/linux-hardened/releases/download/4.19.144.a/linux-hardened-4.19.144.a.patch"
     },
     "5.4": {
-        "name": "linux-hardened-5.4.64.a.patch",
-        "sha256": "1wkkvs66bmgqvgy1iqjck0c0mdad8lnwl42n5npw4ynjhfgiwp3b",
-        "url": "https://github.com/anthraxx/linux-hardened/releases/download/5.4.64.a/linux-hardened-5.4.64.a.patch"
+        "name": "linux-hardened-5.4.67.a.patch",
+        "sha256": "0jpjc1magvlhfwrx43n68xcxxk1g5w2g0rvp92n7yli0db97k1bm",
+        "url": "https://github.com/anthraxx/linux-hardened/releases/download/5.4.67.a/linux-hardened-5.4.67.a.patch"
     },
     "5.7": {
         "name": "linux-hardened-5.7.19.a.patch",
         "sha256": "1lydlh499aj3ck5cnv8q2271y4klvp17zm7j7qni16am14bld936",
         "url": "https://github.com/anthraxx/linux-hardened/releases/download/5.7.19.a/linux-hardened-5.7.19.a.patch"
     },
     "5.8": {
-        "name": "linux-hardened-5.8.10.a.patch",
-        "sha256": "0myfn5iz7gljj977fwsi3vzvm3n66yihrj2w207m3sr9mw9hp6d9",
-        "url": "https://github.com/anthraxx/linux-hardened/releases/download/5.8.10.a/linux-hardened-5.8.10.a.patch"
+        "name": "linux-hardened-5.8.11.a.patch",
+        "sha256": "0cbmlwfzh9ppcvih437sp832rkhr7dfhx97drnkz4gysfyiyh07l",
+        "url": "https://github.com/anthraxx/linux-hardened/releases/download/5.8.11.a/linux-hardened-5.8.11.a.patch"
     }
 }
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
@@ -150,6 +150,8 @@ in {
 
   accupy = callPackage ../development/python-modules/accupy { };
 
+  acebinf = callPackage ../development/python-modules/acebinf { };
+
   acme = callPackage ../development/python-modules/acme { };
 
   acme-tiny = callPackage ../development/python-modules/acme-tiny { };
@@ -979,6 +981,8 @@ in {
 
   bx-python = callPackage ../development/python-modules/bx-python { inherit (pkgs) zlib; };
 
+  bwapy = callPackage ../development/python-modules/bwapy { };
+
   bytecode = callPackage ../development/python-modules/bytecode { };
 
   bz2file = callPackage ../development/python-modules/bz2file { };
@@ -5406,6 +5410,8 @@ in {
 
   pysvn = callPackage ../development/python-modules/pysvn { };
 
+  pytabix = callPackage ../development/python-modules/pytabix { };
+
   pytado = callPackage ../development/python-modules/pytado { };
 
   pytaglib = callPackage ../development/python-modules/pytaglib { };