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diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py
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+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Breakdancer(CMakePackage):
+    """BreakDancer-1.3.6, released under GPLv3, is a perl/Cpp package that
+    provides genome-wide detection of structural variants from next generation
+    paired-end sequencing reads. It includes two complementary programs.
+    BreakDancerMax predicts five types of structural variants: insertions,
+    deletions, inversions, inter- and intra-chromosomal translocations from
+    next-generation short paired-end sequencing reads using read pairs that are
+    mapped with unexpected separation distances or orientation.
+    BreakDancerMini focuses on detecting small indels (usually between 10bp and
+    100bp) using normally mapped read pairs.."""
+
+    homepage = "http://gmt.genome.wustl.edu/packages/breakdancer"
+    url      = "https://github.com/genome/breakdancer/archive/v1.4.5.tar.gz"
+
+    version('1.4.5', sha256='5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6')
+    version('master', submodules='true', 
+            git='https://github.com/genome/breakdancer.git', preferred=True)
+
+    phases = ['edit', 'cmake', 'build', 'install']
+
+    depends_on('zlib')
+
+    depends_on('perl-statistics-descriptive', type='run')
+    depends_on('perl-math-cdf', type='run')
+    depends_on('perl-gd-graph', type='run')
+    depends_on('perl-gdgraph-histogram', type='run')
+    depends_on('perl-list-moreutils', type='run')
+    depends_on('perl-exporter-tiny', type='run')
+
+    # TODO: remove git submodules, and depend on boost & samtools
+
+    parallel = False
+
+    def setup_environment(self, spack_env, run_env):
+        # get the perl tools in the path
+        run_env.prepend_path('PATH', self.prefix.lib)
+
+    def edit(self, spec, prefix):
+        # perl tools end up in a silly lib subdirectory, fixing that
+        filter_file(r'set\(SUPPORT_LIBDIR lib\/breakdancer-max\$ \
+                    \{EXE_VERSION_SUFFIX\}\)',
+                    'set(SUPPORT_LIBDIR lib)',
+                    join_path(self.stage.source_path,
+                              'perl', 'CMakeLists.txt'))