ea-utils: new package (#4690)

* ea-utils: new package

* ea-utils: simplifying self.spec.prefix

* ea-utils: added comment about perl

* ea-utils: fixing flake8 error

1 files changed, 51 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/ea-utils/package.py b/var/spack/repos/builtin/packages/ea-utils/package.py
new file mode 100644
index 0000000000..296b05eaf2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ea-utils/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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 EaUtils(MakefilePackage):
+    """Command-line tools for processing biological sequencing data. Barcode
+       demultiplexing, adapter trimming, etc. Primarily written to support an
+       Illumina based pipeline - but should work with any FASTQs."""
+
+    homepage = "http://expressionanalysis.github.io/ea-utils/"
+    url = "https://github.com/ExpressionAnalysis/ea-utils/archive/1.04.807.tar.gz"
+
+    version('1.04.807', '5972b9f712920603b7527f46c0063a09')
+
+    depends_on('subversion')
+    depends_on('zlib')
+    depends_on('gsl')
+    depends_on('bamtools')
+    # perl module required for make check, which is included in the default
+    # target
+    depends_on('perl', type='build')
+
+    build_directory = 'clipper'
+
+    def edit(self, spec, prefix):
+        with working_dir('clipper'):
+            makefile = FileFilter('Makefile')
+            makefile.filter('/usr', prefix)