express: new package (#6281)

var/spack/repos/builtin/packages/express/package.py

@@ -0,0 +1,63 @@
+##############################################################################
+# 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 *
+import os.path
+import glob
+
+
+class Express(CMakePackage):
+    """eXpress is a streaming tool for quantifying the abundances of a set of
+       target sequences from sampled subsequences."""
+
+    homepage = "http://bio.math.berkeley.edu/eXpress/"
+    url      = "https://github.com/adarob/eXpress"
+
+    version('2015-11-29', commit='f845cab2c7f2d9247b35143e4aa05869cfb10e79',
+            git='https://github.com/adarob/eXpress.git')
+
+    depends_on('boost')
+    depends_on('bamtools')
+    depends_on('zlib')
+
+    conflicts('%gcc@6.0.0:', when='@2015-11-29')
+
+    def patch(self):
+        with working_dir('src'):
+            files = glob.iglob('*.*')
+            for file in files:
+                if os.path.isfile(file):
+                    edit = FileFilter(file)
+                    edit.filter('#include <api', '#include <%s' % self.spec[
+                                'bamtools'].prefix.include.bamtools.api)
+            edit = FileFilter('CMakeLists.txt')
+            # really ugly way to escape the $ in CMakeLists.txt
+            edit.filter('{CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/'
+                        'libbamtools.a', '$')
+            edit.filter('\\$\\$', '%s' % join_path(self.spec[
+                        'bamtools'].prefix.lib.bamtools, 'libbamtools.a'))
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.prepend_path('CPATH', self.spec[
+                               'bamtools'].prefix.include.bamtools)