Merge commit '432fc2d9a67f92e05438dff5fdc2b39d33f77997'

# Conflicts:
#	nixpkgs/pkgs/applications/editors/emacs/elisp-packages/elpa-generated.nix
#	nixpkgs/pkgs/applications/networking/mailreaders/thunderbird/default.nix
#	nixpkgs/pkgs/applications/window-managers/sway/default.nix
#	nixpkgs/pkgs/build-support/rust/default.nix
#	nixpkgs/pkgs/development/go-modules/generic/default.nix

7 files changed, 28 insertions, 22 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix
index 715f5bb8bfa6..205ff9afdca1 100644
--- a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "bowtie2";
-  version = "2.4.2";
+  version = "2.4.4";
 
   src = fetchFromGitHub {
     owner = "BenLangmead";
     repo = pname;
     rev = "v${version}";
-    sha256 = "11apzq7l1lk3yxw97g9dfr0gwnvfh58x6apifcblgd66gbip3y1y";
+    sha256 = "sha256-2B6w6c/qztyBb1jNA0zg+udQm41ouT1DyB6Ygpi5nC8=";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix b/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix
index bed562abe23c..ba1d6c27ccb1 100644
--- a/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages }:
+{ lib, stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages, openmp }:
 
 stdenv.mkDerivation rec {
   version = "4.8.1";
@@ -14,8 +14,12 @@ stdenv.mkDerivation rec {
   propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.PerlMagick ];
 
   nativeBuildInputs = [ zlib makeWrapper ];
+  buildInputs = lib.optional stdenv.cc.isClang openmp;
 
-  makeFlags = [ "PREFIX=$(out)/bin" ];
+  makeFlags = [
+    "CC=${stdenv.cc.targetPrefix}c++" # remove once https://github.com/weizhongli/cdhit/pull/114 is merged
+    "PREFIX=$(out)/bin"
+  ];
 
   preInstall = "mkdir -p $out/bin";
 
diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
index 7ec5476cb826..6224ccabb069 100644
--- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
@@ -6,14 +6,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.20200331";
+  version = "1.0.20210317";
   pname = "dcm2niix";
 
   src = fetchFromGitHub {
     owner = "rordenlab";
     repo = "dcm2niix";
     rev = "v${version}";
-    sha256 = "1cncfwhyhmg18n970lkn6yvp0i74ajznsl8dqz00asqfzmg681n1";
+    sha256 = "05rjk0xsrzcxa979vlx25k1rdz1in84gkfm9l1h9f7k4a4aa5r6j";
   };
 
   nativeBuildInputs = [ cmake git ];
diff --git a/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix b/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix
index 814baa45d8c1..fe4a3e49930c 100644
--- a/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix
@@ -11,6 +11,10 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ gsl ];
 
+  makeFlags = [
+    "CC=${stdenv.cc.targetPrefix}cc"
+  ];
+
   installPhase = ''
     mkdir -p $out/bin
     mkdir -p $out/share/doc/${pname}
diff --git a/nixpkgs/pkgs/applications/science/biology/octopus/default.nix b/nixpkgs/pkgs/applications/science/biology/octopus/default.nix
index b61a0764f2c2..95912d3a7c32 100644
--- a/nixpkgs/pkgs/applications/science/biology/octopus/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/octopus/default.nix
@@ -1,28 +1,16 @@
-{lib, stdenv, fetchpatch, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, xz, pkg-config}:
+{lib, stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, xz, pkg-config}:
 
 stdenv.mkDerivation rec {
   pname = "octopus";
-  version = "0.7.3";
+  version = "0.7.4";
 
   src = fetchFromGitHub {
     owner = "luntergroup";
     repo = "octopus";
     rev = "v${version}";
-    sha256 = "sha256-sPOBZ0YrEdjMNVye/xwqwA5IpsLy2jWN3sm/ce1fLg4=";
+    sha256 = "sha256-FAogksVxUlzMlC0BqRu22Vchj6VX+8yNlHRLyb3g1sE=";
   };
 
-  patches = [
-    # Backport TZ patchs (https://github.com/luntergroup/octopus/issues/149)
-    (fetchpatch {
-      url = "https://github.com/luntergroup/octopus/commit/3dbd8cc33616129ad356e99a4dae82e4f6702250.patch";
-      sha256 = "sha256-UCufVU9x+L1zCEhkr/48KFYRvh8w26w8Jr+O+wULKK8=";
-    })
-    (fetchpatch {
-      url = "https://github.com/luntergroup/octopus/commit/af5a66a2792bd098fb53eb79fb4822625f09305e.patch";
-      sha256 = "sha256-r8jv6EZHfTWVLYUBau3F+ilOd9IeH8rmatorEY5LXP4=";
-    })
-  ];
-
   nativeBuildInputs = [ cmake pkg-config ];
   buildInputs = [ boost gmp htslib zlib xz ];
 
diff --git a/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix b/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix
index 7b5141302f7b..abfac6ce083f 100644
--- a/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, python3, which, ldc, zlib }:
+{ lib, stdenv, fetchFromGitHub, fetchpatch, python3, which, ldc, zlib }:
 
 stdenv.mkDerivation rec {
   pname = "sambamba";
@@ -12,6 +12,14 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
+  patches = [
+    # Fixes hardcoded gcc, making clang build possible.
+    (fetchpatch {
+      url = "https://github.com/biod/sambamba/commit/c50a1c91e1ba062635467f197139bf6784e9be15.patch";
+      sha256 = "1y0vlybmb9wpg4z1nca7m96mk9hxmvd3yrg7w8rxscj45hcqvf8q";
+    })
+  ];
+
   nativeBuildInputs = [ which python3 ldc ];
   buildInputs = [ zlib ];
 
diff --git a/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix b/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix
index 48c19666ba04..4315dd2767e1 100644
--- a/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix
@@ -11,6 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0g24fq5hplnfgqkh3xqpg3lgx3wmxwnh9c7m6yw7pbi40lmgl1jv";
   };
 
+  makeFlags = [ "CPP=${stdenv.cc.targetPrefix}c++" ];
+
   installPhase = ''
     mkdir -p $out/bin
     cp samblaster $out/bin