diff --git a/var/spack/repos/builtin/packages/fastqc/fastqc.patch b/var/spack/repos/builtin/packages/fastqc/fastqc.patch
new file mode 100644
index 0000000000000000000000000000000000000000..a0a1155905f792c05520256ae62423a7fe27b5b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fastqc/fastqc.patch
@@ -0,0 +1,30 @@
+--- fastqc.orig	2015-11-20 09:25:00.000000000 +0000
++++ fastqc	2016-10-24 19:06:16.734000000 +0000
+@@ -38,12 +38,21 @@
+ 	$delimiter = ';';
+ }
+ 
+-if ($ENV{CLASSPATH}) {
+-	$ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
+-}
+-else {
+-	$ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
+-}
++# The lib dir is $RealBin/../lib
++# start with list of jars we need and prefix them with the lib dir
++# then stick CLASSPATH onto the front (empty or otherwise...)
++# then filter out anything that's empty (perhaps CLASSPATH...)
++# then join all the remainings bits with the delimiter.
++use File::Basename;
++use File::Spec::Functions;
++my $_lib = catfile(dirname($RealBin), 'lib');
++$ENV{CLASSPATH} =
++    join($delimiter,
++         grep {$_}
++             ($ENV{CLASSPATH},
++              $_lib,
++              map {"$_lib/$_"}
++                  qw(sam-1.103.jar jbzip2-0.9.jar cisd-jhdf5.jar)));
+ 
+ my @java_args;
+ my @files;
diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..e2a1b54210d272c96fb6b6edca55ef970bee2bf6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fastqc/package.py
@@ -0,0 +1,60 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+from distutils.dir_util import copy_tree, mkpath
+from distutils.file_util import copy_file
+
+
+class Fastqc(Package):
+    """A quality control tool for high throughput sequence data."""
+
+    homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+    url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
+
+    version('0.11.5', '3524f101c0ab0bae77c7595983170a76')
+
+    depends_on('jdk', type='run')
+    depends_on('perl')          # for fastqc "script", any perl will do
+
+    patch('fastqc.patch', level=0)
+
+    def install(self, spec, prefix):
+        mkpath(self.prefix.bin)
+        mkpath(self.prefix.lib)
+        copy_file('fastqc', self.prefix.bin)
+        for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']:
+            copy_file(j, self.prefix.lib)
+        for d in ['Configuration', 'net', 'org', 'Templates', 'uk']:
+            copy_tree(d, join_path(self.prefix.lib, d))
+        chmod = which('chmod')
+        chmod('+x', join_path(self.prefix.bin, 'fastqc'))
+
+    # In theory the 'run' dependency on 'jdk' above should take
+    # care of this for me. In practice, it does not.
+    def setup_environment(self, spack_env, env):
+        """Add <prefix> to the path; the package has a script at the
+           top level.
+        """
+        env.prepend_path('PATH', join_path(self.spec['jdk'].prefix, 'bin'))