new package: homer (starting at 4.9.1) (#9669)

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

@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from os import symlink
+
+
+class Homer(Package):
+    """Software for motif discovery and next generation sequencing analysis"""
+
+    homepage = "http://homer.ucsd.edu/homer"
+    url      = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.zip"
+
+    version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('r-biocgenerics', type='run')
+    depends_on('r-biocparallel', type='run')
+    depends_on('r-edger', type='run')
+    depends_on('r-deseq2', type='run')
+
+    variant('data', default=False,
+            description='Download genome data packages')
+
+    def install(self, spec, prefix):
+        # initialize homer directories
+        basedir = join_path(prefix.lib, 'homer')
+        mkdirp(basedir)
+
+        install_tree('.', basedir)
+
+        # symlink bin so it is included in the PATH
+        symlink(join_path(basedir, 'bin'), prefix.bin)
+
+        # override homer base directory in configure script
+        filter_file('my $homeDir = $1;',
+                    'my $homeDir = \"{0}\";'.format(basedir),
+                    'configureHomer.pl', string=True)
+
+        # compile/prepare binaries and perl scripts with the correct paths
+        perl = which('perl')
+        perl('configureHomer.pl', '-local')
+
+        # download extra data if requested
+        if '+data' in spec:
+            perl('configureHomer.pl', '-install', '-all')