prinseq-lite: Create new package (#7873)

* prinseq-lite: Create new package

* prinseq-lite: set variant description and add dependency type

1 files changed, 60 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/prinseq-lite/package.py b/var/spack/repos/builtin/packages/prinseq-lite/package.py
new file mode 100644
index 0000000000..164044ec96
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prinseq-lite/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 PrinseqLite(Package):
+    """PRINSEQ will help you to preprocess your genomic or metagenomic
+    sequence data in FASTA or FASTQ format."""
+
+    homepage = "http://prinseq.sourceforge.net"
+    url      = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz"
+
+    version('0.20.4', '3be1a572073ebbbecfeba42a42853ff5')
+
+    variant('nopca', default=True, description="Graphs version without PCA")
+
+    depends_on('perl', type='run')
+    depends_on('perl-cairo', type='run')
+    depends_on('perl-digest-md5', type='run')
+    depends_on('perl-json', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'prinseq-graphs-noPCA.pl')
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'prinseq-lite.pl')
+
+        install('prinseq-graphs-noPCA.pl', prefix.bin)
+        install('prinseq-lite.pl', prefix.bin)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(self.prefix.bin, 'prinseq-graphs-noPCA.pl'))
+        chmod('+x', join_path(self.prefix.bin, 'prinseq-lite.pl'))