diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix
index fb7f2cba3de3..e641489b86c9 100644
--- a/pkgs/applications/science/biology/hisat2/default.nix
+++ b/pkgs/applications/science/biology/hisat2/default.nix
@@ -1,16 +1,18 @@
-{stdenv, fetchurl, unzip, which, python, perl}:
+{stdenv, fetchFromGitHub, unzip, which, python3, perl}:
 
 stdenv.mkDerivation rec {
   pname = "hisat2";
-  version = "2.1.0";
+  version = "2.2.1";
 
-  src = fetchurl {
-    url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-${version}-source.zip";
-    sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
+  src = fetchFromGitHub {
+    owner = "DaehwanKimLab";
+    repo = "hisat2";
+    rev = "v${version}";
+    sha256 = "0lmzdhzjkvxw7n5w40pbv5fgzd4cz0f9pxczswn3d4cr0k10k754";
   };
 
   nativeBuildInputs = [ unzip which ];
-  buildInputs = [ python perl ];
+  buildInputs = [ python3 perl ];
 
   installPhase = ''
     mkdir -p $out/bin
@@ -30,12 +32,6 @@ stdenv.mkDerivation rec {
        hisat2_extract_snps_haplotypes_VCF.py \
        hisat2_extract_splice_sites.py \
        hisat2_simulate_reads.py \
-       hisatgenotype_build_genome.py \
-       hisatgenotype_extract_reads.py \
-       hisatgenotype_extract_vars.py \
-       hisatgenotype_hla_cyp.py \
-       hisatgenotype_locus.py \
-       hisatgenotype.py \
        $out/bin
   '';