7 files changed, 40 insertions, 12 deletions
diff --git a/lib/maintainers.nix b/lib/maintainers.nix
index 5614627db0d8..ba5ee757a7cd 100644
--- a/lib/maintainers.nix
+++ b/lib/maintainers.nix
@@ -55,6 +55,7 @@
   antonxy = "Anton Schirg <anton.schirg@posteo.de>";
   apeschar = "Albert Peschar <albert@peschar.net>";
   apeyroux = "Alexandre Peyroux <alex@px.io>";
+  arcadio = "Arcadio Rubio García <arc@well.ox.ac.uk>";
   ardumont = "Antoine R. Dumont <eniotna.t@gmail.com>";
   aristid = "Aristid Breitkreuz <aristidb@gmail.com>";
   arobyn = "Alexei Robyn <shados@shados.net>";
diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix
index a2a40f0acc80..13cb407391c0 100644
--- a/pkgs/applications/science/biology/igv/default.nix
+++ b/pkgs/applications/science/biology/igv/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "igv-${version}";
-  version = "2.3.98";
+  version = "2.4.6";
 
   src = fetchurl {
-    url = "http://data.broadinstitute.org/igv/projects/downloads/IGV_${version}.zip";
-    sha256 = "1bjdsvx8jsbcry6v7yfclh3vrlsvaw38f3s9587lklj63zj638l2";
+    url = "http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip";
+    sha256 = "00p9xhfn6snzm31q9l3dxccsj7rhlci8n3pgpy3k67q91mi2hkna";
   };
 
   buildInputs = [ unzip jre ];
diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix
new file mode 100644
index 000000000000..d80ffea9a780
--- /dev/null
+++ b/pkgs/applications/science/biology/kallisto/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, fetchFromGitHub, cmake, hdf5, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "kallisto-${version}";
+  version = "0.43.1";
+
+  src = fetchFromGitHub {
+    repo = "kallisto";
+    owner = "pachterlab";
+    rev = "v${version}";
+    sha256 = "04697pf7jvy7vw126s1rn09q4iab9223jvb1nb0jn7ilwkq7pgwz";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  
+  buildInputs = [ hdf5 zlib ];
+
+  meta = with stdenv.lib; {
+    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 ];
+  };
+}
diff --git a/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix b/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
index cf4d5bcaa40c..e7c2509ce771 100644
--- a/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
+++ b/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
@@ -1,16 +1,16 @@
 { lib, buildGoPackage, fetchFromGitLab, fetchurl, go-bindata }:
 
 let
-  version = "10.3.0";
+  version = "10.4.0";
   # Gitlab runner embeds some docker images these are prebuilt for arm and x86_64
   docker_x86_64 = fetchurl {
     url = "https://gitlab-runner-downloads.s3.amazonaws.com/v${version}/docker/prebuilt-x86_64.tar.xz";
-    sha256 = "0nhxxx2wxnli5nfz8vxqc0mwdjzj836zx3zmywnfyy1k2zybjijv";
+    sha256 = "0fcddi1mwgj831abn628zcpwsah3mmvrbdi851pjf8vraynwr2xa";
   };
 
   docker_arm = fetchurl {
     url = "https://gitlab-runner-downloads.s3.amazonaws.com/v${version}/docker/prebuilt-arm.tar.xz";
-    sha256 = "0jacimz4p9k5s9j510g3vn7gg8pybpa20j4cvz4pffrcwl1lgk4i";
+    sha256 = "1zlk3i9jzmsqz5r3kzg08z9hyhidw9dpv5ji46bnbjis8q3dlw54";
   };
 in
 buildGoPackage rec {
@@ -29,7 +29,7 @@ buildGoPackage rec {
     owner = "gitlab-org";
     repo = "gitlab-runner";
     rev = "v${version}";
-    sha256 = "0wjy5bbz6bw0na57vglcwzn17q980x6j24qkschqx49rjyk3fz2i";
+    sha256 = "0kp6h53d1q652i4wp94hydy1ixlgmqh92sjsc6pqicnfc7nvwgfq";
   };
 
   patches = [ ./fix-shell-path.patch ];
diff --git a/pkgs/development/tools/dep/default.nix b/pkgs/development/tools/dep/default.nix
index e22be524f021..630b1396944d 100644
--- a/pkgs/development/tools/dep/default.nix
+++ b/pkgs/development/tools/dep/default.nix
@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "dep-${version}";
-  version = "0.3.1";
+  version = "0.4.0";
   rev = "v${version}";
 
   goPackagePath = "github.com/golang/dep";
@@ -12,7 +12,7 @@ buildGoPackage rec {
     inherit rev;
     owner = "golang";
     repo = "dep";
-    sha256 = "0dsiaqfrp7ihhx10qapkl6zm3dw3rwdgcr9rkvmq8zprcp7njz90";
+    sha256 = "1m325p1brzhqkabibc1ifvrsa589m0077z33l3hzq6ml88qm6nyp";
   };
 
   buildFlagsArray = ("-ldflags=-s -w -X main.commitHash=${rev} -X main.version=${version}");
diff --git a/pkgs/misc/emulators/citra/default.nix b/pkgs/misc/emulators/citra/default.nix
index 97f61e452ff2..2eebe089de32 100644
--- a/pkgs/misc/emulators/citra/default.nix
+++ b/pkgs/misc/emulators/citra/default.nix
@@ -1,13 +1,13 @@
 { stdenv, fetchgit, cmake, SDL2, qtbase, boost, curl, gtest }:
 
 stdenv.mkDerivation rec { 
-  name = "citra-2017-07-26";
+  name = "citra-2018-01-24";
 
   # Submodules
   src = fetchgit {
     url = "https://github.com/citra-emu/citra";
-    rev = "a724fb365787718f9e44adedc14e59d0854905a6";
-    sha256 = "0lkrwhxvq85c0smix27xvj8m463bxa67qhy8m8r43g39n0h8d5sf";
+    rev = "33b0b5163fdb08bc8aa1d7eb83e0931a14ed3046";
+    sha256 = "07z32d8lj84yy3l5iqpk37mnmvzjmppqhyqr64kbx14dh5hb6cbj";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 4b3a5223f10e..a48f43fc9ffe 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -18945,6 +18945,8 @@ with pkgs;
     neuron-version = neuron.version;
   };
 
+  kallisto = callPackage ../applications/science/biology/kallisto { };
+
   neuron = callPackage ../applications/science/biology/neuron {
     python = null;
   };