Features/pindel (#7619)

* added htslib 1.7 and checksum

* pindel:  added new package pindel

* pindel: added package pindel

* removed py-pybind11 edit

* made flake8 happy

* fixed additional flake8 errors

* added comments about Makefile2 and removed FIXME template section

* spelling

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

@@ -0,0 +1,74 @@
+##############################################################################
+# 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 *
+from shutil import copytree, copyfile
+
+
+class Pindel(MakefilePackage):
+    """Pindel can detect breakpoints from next-gen sequence data."""
+
+    homepage = "http://gmt.genome.wustl.edu/packages/pindel/"
+    url      = "https://github.com/genome/pindel/archive/v0.2.5.tar.gz"
+
+    version('0.2.5b8', 'e6de2ffb38ba1cb89351cdccabe78cde')
+    version('0.2.5b6', 'dc2febb18c203f0ef1ba02b7b882e94b')
+    version('0.2.5b5', '73e964bc19de9ab9e6e8a316353e3184')
+    version('0.2.5b4', 'b4aefd538d9f62578f46440c4bce497e')
+    version('0.2.5b1', 'a8e53e8919aa29093db13fad5ede93a5')
+    version('0.2.5a7', '5fb2bac6108547b5d60c38fc66abdfc4')
+    version('0.2.5',   'd4568cbb83ec25ef9f9f6f058b30053e')
+
+    depends_on('htslib@1.7:')
+    #
+    # This Makefile2 stuff is due to the original installer,
+    # The author wants to run make twice, the first
+    # time generates a Makefile.local then returns "false"
+    # User is then suppose to run make again and the
+    # package will compile. This is an attempt to
+    # stay as close to the original installer as possible
+    #
+
+    def edit(self, spec, prefix):
+        makefile2 = join_path(self.build_directory, 'Makefile2')
+        copyfile(join_path(self.build_directory, 'Makefile'), makefile2)
+        myedit = FileFilter(makefile2)
+        myedit.filter('-include Makefile.local', '#removed include')
+        myedit.filter('@false', '#removed autofailure')
+
+    def build(self, spec, prefix):
+        make("Makefile.local", "-f",
+             "Makefile2",
+             "HTSLIB=%s" % spec['htslib'].prefix)
+        make("HTSLIB=%s" % spec['htslib'].prefix)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('src/pindel', prefix.bin)
+        install('src/pindel2vcf', prefix.bin)
+        install('src/sam2pindel', prefix.bin)
+        install('src/pindel2vcf4tcga', prefix.bin)
+        copytree(join_path(self.build_directory, 'demo'),
+                 prefix.doc,
+                 symlinks=True)