Merge branch 'master' into staging

2 files changed, 13 insertions, 8 deletions

diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix
index 16639db17816..de93ae5d7829 100644
--- a/pkgs/applications/science/biology/kallisto/default.nix
+++ b/pkgs/applications/science/biology/kallisto/default.nix
@@ -1,25 +1,28 @@
-{ stdenv, fetchFromGitHub, cmake, hdf5, zlib }:
+{ stdenv, fetchFromGitHub, autoconf, cmake, hdf5, zlib }:
 
 stdenv.mkDerivation rec {
   pname = "kallisto";
-  version = "0.43.1";
+  version = "0.46.0";
 
   src = fetchFromGitHub {
     repo = "kallisto";
     owner = "pachterlab";
     rev = "v${version}";
-    sha256 = "04697pf7jvy7vw126s1rn09q4iab9223jvb1nb0jn7ilwkq7pgwz";
+    sha256 = "09vgdqwpigl4x3sdw5vjfyknsllkli339mh8xapbf7ldm0jldfn9";
   };
 
-  nativeBuildInputs = [ cmake ];
-  
+  nativeBuildInputs = [ autoconf cmake ];
+
   buildInputs = [ hdf5 zlib ];
 
+  # Parallel build fails in some cases: https://github.com/pachterlab/kallisto/issues/160
+  enableParallelBuilding = false;
+
   meta = with stdenv.lib; {
-    description = "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data";
-    homepage = https://pachterlab.github.io/kallisto;
+    description = "Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data";
+    homepage = "https://pachterlab.github.io/kallisto";
     license = licenses.bsd2;
     platforms = platforms.linux;
-    maintainers = [ maintainers.arcadio ];
+    maintainers = with maintainers; [ arcadio ];
   };
 }
diff --git a/pkgs/applications/science/logic/symbiyosys/default.nix b/pkgs/applications/science/logic/symbiyosys/default.nix
index a5be51a6025a..ed66c77dcabf 100644
--- a/pkgs/applications/science/logic/symbiyosys/default.nix
+++ b/pkgs/applications/science/logic/symbiyosys/default.nix
@@ -26,6 +26,8 @@ stdenv.mkDerivation {
     substituteInPlace $out/bin/sby \
       --replace "##yosys-sys-path##" \
                 "sys.path += [p + \"/share/yosys/python3/\" for p in [\"$out\", \"${yosys}\"]]"
+    substituteInPlace $out/share/yosys/python3/sby_core.py \
+      --replace '"/usr/bin/env", "bash"' '"${bash}/bin/bash"'
   '';
   meta = {
     description = "Tooling for Yosys-based verification flows";