1 files changed, 56 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/bracken/package.py b/var/spack/repos/builtin/packages/bracken/package.py
new file mode 100644
index 0000000000..ed48722a59
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+++ b/var/spack/repos/builtin/packages/bracken/package.py
@@ -0,0 +1,56 @@
+# 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 Bracken(Package):
+    """Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly
+    accurate statistical method that computes the abundance of species in DNA
+    sequences from a metagenomics sample."""
+
+    homepage = "https://ccb.jhu.edu/software/bracken"
+    url      = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz"
+
+    version('1.0.0', 'bd91805655269c5f3becb8f8028bab6d')
+
+    depends_on('perl')
+    depends_on('python@2.7:')
+    depends_on('perl-exporter-tiny')
+    depends_on('perl-list-moreutils')
+    depends_on('perl-parallel-forkmanager')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('sample_data', prefix.sample_data)
+
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'count-kmer-abundances.pl'
+        )
+
+        filter_file(
+            r'#!/usr/bin/python',
+            '#!/usr/bin/env python',
+            'est_abundance.py'
+        )
+
+        filter_file(
+            r'#!/usr/bin/python',
+            '#!/usr/bin/env python',
+            'generate_kmer_distribution.py'
+        )
+
+        files = (
+            'count-kmer-abundances.pl',
+            'est_abundance.py',
+            'generate_kmer_distribution.py',
+        )
+
+        chmod = which('chmod')
+        for name in files:
+            install(name, prefix.bin)
+            chmod('+x', join_path(self.prefix.bin, name))