From 295cdc5674fe63ebf5717fc0053913b80ec76ceb Mon Sep 17 00:00:00 2001
From: Audrey Thoma <las_thoma15@iastate.edu>
Date: Fri, 11 Aug 2017 13:50:08 -0500
Subject: [PATCH] gapfiller: new package (#5073)

---
 .../builtin/packages/gapfiller/package.py     | 52 +++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gapfiller/package.py

diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py
new file mode 100644
index 0000000000..766c51d42d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gapfiller/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# 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 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 *
+import os
+
+
+class Gapfiller(Package):
+    """GapFiller is a stand-alone program for closing gaps within
+       pre-assembled scaffolds.
+
+       Note: A manual download is required for GapFiller.
+       Spack will search your current directory for the download file.
+       Alternatively, add this file to a mirror so that Spack can find it.
+       For instructions on how to set up a mirror, see
+       http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller"
+
+    version('1.10', '54d5e2ada131a1305a66e41c0d380382')
+
+    def url_for_version(self, version):
+        return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
+                os.getcwd(), version.dashed)
+
+    depends_on('perl', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        install_tree('bowtie', prefix.bowtie)
+        install_tree('bwa', prefix.bwa)
+        install('GapFiller.pl', prefix)