new package: deconseq-standalone (#7290)

var/spack/repos/builtin/packages/deconseq-standalone/package.py

@@ -0,0 +1,60 @@
+##############################################################################
+# 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 DeconseqStandalone(Package):
+    """The DeconSeq tool can be used to automatically detect and efficiently
+    remove sequence contaminations from genomic and metagenomic datasets."""
+
+    homepage = "http://deconseq.sourceforge.net"
+    url      = "https://sourceforge.net/projects/deconseq/files/standalone/deconseq-standalone-0.4.3.tar.gz"
+
+    version('0.4.3', 'cb3fddb90e584d89fd9c2b6b8f2e20a2')
+
+    depends_on('perl@5:')
+
+    def install(self, spec, prefix):
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl', 'deconseq.pl')
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl', 'splitFasta.pl')
+
+        mkdirp(prefix.bin)
+        install('bwa64', prefix.bin)
+        install('bwaMAC', prefix.bin)
+        install('deconseq.pl', prefix.bin)
+        install('splitFasta.pl', prefix.bin)
+        install('DeconSeqConfig.pm', prefix)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix.bin, 'bwa64'))
+        chmod('+x', join_path(prefix.bin, 'bwaMAC'))
+        chmod('+x', join_path(prefix.bin, 'deconseq.pl'))
+        chmod('+x', join_path(prefix.bin, 'splitFasta.pl'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PERL5LIB', prefix)