bracken: Create new package (#7375)

var/spack/repos/builtin/packages/bracken/package.py

@@ -0,0 +1,75 @@
+##############################################################################
+# 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/spack/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 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))