nixpkgs: merge nixos-unstable

9 files changed, 15 insertions, 19 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/blast/default.nix b/nixpkgs/pkgs/applications/science/biology/blast/default.nix
index 6fd061f1402d..877b5b7d34c0 100644
--- a/nixpkgs/pkgs/applications/science/biology/blast/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/blast/default.nix
@@ -1,12 +1,12 @@
-{ lib, stdenv, fetchurl, zlib, bzip2, perl, cpio, gawk, coreutils, ApplicationServices }:
+{ lib, stdenv, buildPackages, fetchurl, zlib, bzip2, perl, cpio, gawk, coreutils, ApplicationServices }:
 
 stdenv.mkDerivation rec {
   pname = "blast";
-  version = "2.10.0";
+  version = "2.11.0";
 
   src = fetchurl {
-    url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz";
-    sha256 = "09nry5knj5hhxpn0a5ww1gb1704grd4r1y7adbjl6kqwq37dkk9s";
+    url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz";
+    sha256 = "0m0r9vkw631ky1za1wilsfk9k9spwqh22nkrb9a57rbwmrc1i3nq";
   };
 
   sourceRoot = "ncbi-blast-${version}+-src/c++";
@@ -75,6 +75,7 @@ stdenv.mkDerivation rec {
         --replace /bin/date ${coreutils}/bin/date
   '';
 
+  depsBuildBuild = [ buildPackages.stdenv.cc ];
   nativeBuildInputs = [ perl ];
 
   # perl is necessary in buildInputs so that installed perl scripts get patched
diff --git a/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch b/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch
index 9b78ac579264..851e37fa905d 100644
--- a/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch
+++ b/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch
@@ -171,14 +171,8 @@ diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.
  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 $LN_S" >&6; }
- fi
- 
+@@ -10417,4 +10417,0 @@
 -case "$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/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix b/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix
index c6defb245c7f..7eb3afd437af 100644
--- a/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, fetchpatch, makeWrapper, python27Packages, wget, diamond, hmmer }:
+{ lib, fetchFromGitHub, fetchpatch, makeWrapper, python27Packages, wget, diamond, hmmer }:
 
 python27Packages.buildPythonApplication rec {
   pname = "eggnog-mapper";
diff --git a/nixpkgs/pkgs/applications/science/biology/obitools/obitools3.nix b/nixpkgs/pkgs/applications/science/biology/obitools/obitools3.nix
index 55a9612c62d0..082a779e12bf 100644
--- a/nixpkgs/pkgs/applications/science/biology/obitools/obitools3.nix
+++ b/nixpkgs/pkgs/applications/science/biology/obitools/obitools3.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, python3Packages, cmake, python3 }:
+{ lib, fetchurl, python3Packages, cmake, python3 }:
 
 let
   pythonPackages = python3Packages;
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index 4a3816c4d4af..52a17e8d01cd 100644
--- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "picard-tools";
-  version = "2.24.1";
+  version = "2.25.0";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "sha256-acCsYHyZ358hYqa2haOxR+g6FQGtK+hstYfLBvHLwR8=";
+    sha256 = "sha256-+vJDTahP4htRbVeBd2eSD97fwZ69wB2cro1tMxT36Jc=";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/biology/poretools/default.nix b/nixpkgs/pkgs/applications/science/biology/poretools/default.nix
index 454843e2f324..b2cefefb5cb5 100755
--- a/nixpkgs/pkgs/applications/science/biology/poretools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/poretools/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, pythonPackages, fetchFromGitHub }:
+{ lib, pythonPackages, fetchFromGitHub }:
 
 pythonPackages.buildPythonPackage rec {
   pname = "poretools";
diff --git a/nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix b/nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix
index 2efa39ac489d..11530c6a7226 100644
--- a/nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix
@@ -41,5 +41,6 @@ stdenv.mkDerivation rec {
     platforms = platforms.x86_64;
     homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/";
     maintainers = with maintainers; [ luispedro ];
+    broken = stdenv.isDarwin;
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/biology/star/default.nix b/nixpkgs/pkgs/applications/science/biology/star/default.nix
index a7fe948ecfd6..345863847377 100644
--- a/nixpkgs/pkgs/applications/science/biology/star/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/star/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "star";
-  version = "2.7.6a";
+  version = "2.7.7a";
 
   src = fetchFromGitHub {
     repo = "STAR";
     owner = "alexdobin";
     rev = version;
-    sha256 = "1zw9f4jbhz0y51namnmid42pa7pviviy94q9db8w0774nksdf8is";
+    sha256 = "sha256-0K49yjcnTzC56ZIB20OeTiMJ5EW8mRx+xEpyWEfFcts=";
   };
 
   sourceRoot = "source/source";
diff --git a/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix b/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix
index b70ac29e38f7..cb606a6b3463 100644
--- a/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
+{ lib, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
 , samtools, findutils, python }:
 
 python3Packages.buildPythonApplication rec {