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diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py
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+##############################################################################
+# Copyright (c) 2013-2017, 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 NOTICE and LICENSE files 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 *
+
+
+class Scalpel(MakefilePackage):
+    """Scalpel is a software package for detecting INDELs (INsertions and
+       DELetions) mutations in a reference genome which has been sequenced
+       with next-generation sequencing technology.
+    """
+
+    homepage = "http://scalpel.sourceforge.net/index.html"
+    url      = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz"
+
+    version('0.5.3', '682c9f1cd6ab2cb11c6866f303c673f0')
+
+    depends_on('cmake')
+    depends_on('perl@5.10.0:')
+
+    # bamtools needs to build before the others.
+    parallel = False
+
+    @run_before('install')
+    def filter_sbang(self):
+        """Run before install so that the standard Spack sbang install hook
+        can fix up the path to the perl|python binary.
+        """
+
+        with working_dir(self.stage.source_path):
+            kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
+
+            match = '^#!/usr/bin/env perl'
+            perl = self.spec['perl'].command
+            substitute = "#!{perl}".format(perl=perl)
+            files = ['FindDenovos.pl', 'scalpel-export',
+                     'scalpel-discovery', 'FindVariants.pl',
+                     'FindSomatic.pl']
+            filter_file(match, substitute, *files, **kwargs)
+
+    # Scalpel doesn't actually *have* an install step.  The authors
+    # expect you to unpack the tarball, build it in the resulting
+    # directory, and add that directory to your PATH.  The Perl
+    # scripts use `FindBin` to discover the directory in which they
+    # live and they run their own dedicated copies of {bam,sam}tools
+    # and etc... by explicitly naming the executables in their directory.
+    #
+    # Rather than trying to fix their code I just copied the juicy
+    # bits into prefix.bin. It's not normal, but....
+    #
+    def install(self, spec, prefix):
+        destdir = prefix.bin    # see the note above....
+
+        mkdirp(destdir)
+
+        files = ['FindSomatic.pl', 'HashesIO.pm', 'MLDBM.pm',
+                 'scalpel-export', 'Utils.pm', 'FindDenovos.pl',
+                 'FindVariants.pl', 'scalpel-discovery',
+                 'SequenceIO.pm', 'Usage.pm']
+        for f in files:
+            install(f, destdir)
+
+        dirs = ['Text',  'MLDBM', 'Parallel', ]
+        for d in dirs:
+            install_tree(d, join_path(destdir, d))
+
+        install_tree('bamtools-2.3.0/bin',
+                     join_path(destdir, 'bamtools-2.3.0', 'bin'))
+        install_tree('bamtools-2.3.0/lib',
+                     join_path(destdir, 'bamtools-2.3.0', 'lib'))
+
+        mkdirp(join_path(destdir, 'bcftools-1.1'))
+        install('bcftools-1.1/bcftools', join_path(destdir, 'bcftools-1.1'))
+
+        mkdirp(join_path(destdir, 'Microassembler'))
+        install('Microassembler/Microassembler',
+                join_path(destdir, 'Microassembler'))
+
+        mkdirp(join_path(destdir, 'samtools-1.1'))
+        install('samtools-1.1/samtools', join_path(destdir, 'samtools-1.1'))