portcullis: new package starting at 1.1.2 (#9218)

1 files changed, 73 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/portcullis/package.py b/var/spack/repos/builtin/packages/portcullis/package.py
new file mode 100644
index 0000000000..24ec56fdc3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/portcullis/package.py
@@ -0,0 +1,73 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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 *
+
+
+class Portcullis(AutotoolsPackage):
+    """PORTable CULLing of Invalid Splice junctions"""
+
+    homepage = "https://github.com/maplesond/portcullis"
+    url      = "https://github.com/maplesond/portcullis/archive/Release-1.1.2.tar.gz"
+
+    version('1.1.2', '5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749')
+
+    depends_on('autoconf@2.53:', type='build')
+    depends_on('automake@1.11:', type='build')
+    depends_on('libtool@2.4.2:',  type='build')
+    depends_on('m4', type='build')
+
+    depends_on('zlib', type='build')
+    depends_on('samtools', type='build')
+
+    depends_on('python@3.4:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-pandas', type=('build', 'run'))
+
+    # later versions of py-sphinx don't get detected by the configure script
+    depends_on('py-sphinx@1.3:1.4')
+
+    def patch(self):
+        # remove static linking to libstdc++
+        filter_file(
+            'AM_LDFLAGS="-static-libstdc++"',
+            'AM_LDFLAGS=""',
+            'configure.ac', string=True
+        )
+
+        # prevent install scripts from ruining our PYTHONPATH
+        filter_file(
+            'export PYTHONPATH=$(DESTDIR)$(pythondir)',
+            'export PYTHONPATH="$(PYTHONPATH):$(DESTDIR)$(pythondir)"',
+            'scripts/Makefile.am', string=True
+        )
+
+    def build(self, spec, prefix):
+        # build manpages
+        make('man')
+
+        # run boost build script
+        sh = which('sh')
+        sh('build_boost.sh')