From 8297244446e5505c888cf462442af3b9d5de0932 Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Tue, 30 May 2017 04:59:37 -0700
Subject: Add package for vcftools@0.1.14 (#4389)

* Add package for vcftools@0.1.14

The package munges the various perl scripts so that their sbang lines
point to the depended upon perl (perhaps with Spack sbanger in the
dance) instead of relying on `/usr/bin/env perl`.

As it stands it installs its Perl libraries into `prefix/lib` and then
depends on `setup_environment` to prepend that dir onto PERL5LIB.

See my [vcftools issue
80](https://github.com/vcftools/vcftools/issues/80) for a discussion
about fixing its non-functional attempt at isolating itself from
PERL5LIB shenanigans.

* perl dependency should be build/run
---
 .../repos/builtin/packages/vcftools/package.py     | 75 ++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/vcftools/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/vcftools/package.py b/var/spack/repos/builtin/packages/vcftools/package.py
new file mode 100644
index 0000000000..3f2f01dbff
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vcftools/package.py
@@ -0,0 +1,75 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 Vcftools(AutotoolsPackage):
+    """VCFtools is a program package designed for working with VCF files,
+       such as those generated by the 1000 Genomes Project. The aim of
+       VCFtools is to provide easily accessible methods for working
+       with complex genetic variation data in the form of VCF files.
+    """
+
+    homepage = "https://vcftools.github.io/"
+    url      = "https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz"
+
+    # this is "a pre-release"
+    # version('0.1.15', '61045197848dea20a0158d2faf02e5be')
+    version('0.1.14', 'a110662535651caa6cc8c876216a9f77')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('zlib')
+
+    # this needs to be in sync with what setup_environment adds to
+    # PERL5LIB below
+    def configure_args(self):
+        return ['--with-pmdir=lib']
+
+    @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 binary.
+        """
+
+        with working_dir('src/perl'):
+            match = '^#!/usr/bin/env perl'
+            perl = join_path(self.spec['perl'].prefix.bin, 'perl')
+            substitute = "#!{perl}".format(perl=perl)
+            # tab-to-vcf added in 0.1.15
+            files = ['fill-aa', 'fill-an-ac', 'fill-fs',
+                     'fill-ref-md5', 'tab-to-vcf', 'vcf-annotate',
+                     'vcf-compare', 'vcf-concat', 'vcf-consensus',
+                     'vcf-contrast', 'vcf-convert',
+                     'vcf-fix-newlines', 'vcf-fix-ploidy',
+                     'vcf-indel-stats', 'vcf-isec', 'vcf-merge',
+                     'vcf-phased-join', 'vcf-query',
+                     'vcf-shuffle-cols', 'vcf-sort', 'vcf-stats',
+                     'vcf-subset', 'vcf-to-tab', 'vcf-tstv',
+                     'vcf-validator', ]
+            kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
+            filter_file(match, substitute, *files, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PERL5LIB', join_path(self.prefix, 'lib'))
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