sabre (#4619)

* sabre initial commit, works but test does not

* removing test until I have time to fix it

* sabre: fixing flake8 errors

* sabre: changing to MakefilePackage

1 files changed, 48 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/sabre/package.py b/var/spack/repos/builtin/packages/sabre/package.py
new file mode 100644
index 0000000000..ecee1012f5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sabre/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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/llnl/spack
+# Please also see the LICENSE file 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 Sabre(MakefilePackage):
+    """Sabre is a tool that will demultiplex barcoded reads into separate
+       files. It will work on both single-end and paired-end data in fastq
+       format. It simply compares the provided barcodes with each read and
+       separates the read into its appropriate barcode file, after stripping
+       the barcode from the read (and also stripping the quality values of
+       the barcode bases). If a read does not have a recognized barcode,
+       then it is put into the unknown file.
+    """
+
+    homepage = "https://github.com/najoshi/sabre"
+    url = "https://github.com/najoshi/sabre"
+
+    version('2013-09-27', git='https://github.com/najoshi/sabre.git', commit='039a55e500ba07b7e6432ea6ec2ddcfb3471d949')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('sabre', prefix.bin)