Add package for scalpel@0.5.3 (#5901)

* Add package for scalpel@0.5.3

Scalpel's a bit of a mess, it expects it's users to just unpack the
tarball, build it in the resulting directory and install that
directory onto their PATH.  My install step recapitulates this into
prefix.bin.  The alternative was rewiring their scripts (perl), which
use `FindBin` and expect things to be located in the same dir that the
script itself is.

Sigh.

Lightly tested on CentOS 7.

* Flake8 cleanup

* Additional flake8 cleanup

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

@@ -0,0 +1,101 @@
+##############################################################################
+# 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/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 Scalpel(MakefilePackage):
+    """Scalpel is a software package for detecting INDELs (INsertions and
+       DELetions) mutations in a reference genome which has been sequenced
+       with next-generation sequencing technology.
+    """
+
+    homepage = "http://scalpel.sourceforge.net/index.html"
+    url      = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz"
+
+    version('0.5.3', '682c9f1cd6ab2cb11c6866f303c673f0')
+
+    depends_on('cmake')
+    depends_on('perl@5.10.0:')
+
+    # bamtools needs to build before the others.
+    parallel = False
+
+    @run_before('install')
+    def filter_sbang(self):
+        """Run before install so that the standard Spack sbang install hook
+        can fix up the path to the perl|python binary.
+        """
+
+        with working_dir(self.stage.source_path):
+            kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
+
+            match = '^#!/usr/bin/env perl'
+            perl = self.spec['perl'].command
+            substitute = "#!{perl}".format(perl=perl)
+            files = ['FindDenovos.pl', 'scalpel-export',
+                     'scalpel-discovery', 'FindVariants.pl',
+                     'FindSomatic.pl']
+            filter_file(match, substitute, *files, **kwargs)
+
+    # Scalpel doesn't actually *have* an install step.  The authors
+    # expect you to unpack the tarball, build it in the resulting
+    # directory, and add that directory to your PATH.  The Perl
+    # scripts use `FindBin` to discover the directory in which they
+    # live and they run their own dedicated copies of {bam,sam}tools
+    # and etc... by explicitly naming the executables in their directory.
+    #
+    # Rather than trying to fix their code I just copied the juicy
+    # bits into prefix.bin. It's not normal, but....
+    #
+    def install(self, spec, prefix):
+        destdir = prefix.bin    # see the note above....
+
+        mkdirp(destdir)
+
+        files = ['FindSomatic.pl', 'HashesIO.pm', 'MLDBM.pm',
+                 'scalpel-export', 'Utils.pm', 'FindDenovos.pl',
+                 'FindVariants.pl', 'scalpel-discovery',
+                 'SequenceIO.pm', 'Usage.pm']
+        for f in files:
+            install(f, destdir)
+
+        dirs = ['Text',  'MLDBM', 'Parallel', ]
+        for d in dirs:
+            install_tree(d, join_path(destdir, d))
+
+        install_tree('bamtools-2.3.0/bin',
+                     join_path(destdir, 'bamtools-2.3.0', 'bin'))
+        install_tree('bamtools-2.3.0/lib',
+                     join_path(destdir, 'bamtools-2.3.0', 'lib'))
+
+        mkdirp(join_path(destdir, 'bcftools-1.1'))
+        install('bcftools-1.1/bcftools', join_path(destdir, 'bcftools-1.1'))
+
+        mkdirp(join_path(destdir, 'Microassembler'))
+        install('Microassembler/Microassembler',
+                join_path(destdir, 'Microassembler'))
+
+        mkdirp(join_path(destdir, 'samtools-1.1'))
+        install('samtools-1.1/samtools', join_path(destdir, 'samtools-1.1'))