preseq: new package (#5122)

1 files changed, 44 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/preseq/package.py b/var/spack/repos/builtin/packages/preseq/package.py
new file mode 100644
index 0000000000..87779bcbac
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+++ b/var/spack/repos/builtin/packages/preseq/package.py
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+##############################################################################
+# 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 *
+
+
+class Preseq(MakefilePackage):
+    """The preseq package is aimed at predicting and estimating the complexity
+       of a genomic sequencing library, equivalent to predicting and
+       estimating the number of redundant reads from a given sequencing depth
+       and how many will be expected from additional sequencing using an
+       initial sequencing experiment."""
+
+    homepage = "https://github.com/smithlabcode/preseq"
+    url      = "https://github.com/smithlabcode/preseq/releases/download/v2.0.2/preseq_v2.0.2.tar.bz2"
+
+    version('2.0.2', '9f2a7b597c9f08b821db6ee55e2ea39c')
+
+    depends_on('samtools')
+    depends_on('gsl')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('PREFIX', self.prefix)