adding perl-bio-perl and dependencies (#5845)

* perl-bio-perl and dependencies

* minor fixes

* condensing code

* fixing doc error

11 files changed, 428 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py
new file mode 100644
index 0000000000..bfcdd05b1f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# 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 PerlAlgorithmDiff(PerlPackage):
+    """Compute 'intelligent' differences between two files / lists"""
+
+    homepage = "http://search.cpan.org/~tyemq/Algorithm-Diff-1.1903/lib/Algorithm/Diff.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/T/TY/TYEMQ/Algorithm-Diff-1.1903.tar.gz"
+
+    version('1.1903', '0e8add21a641b8d66436df0c2024bf3b')
diff --git a/var/spack/repos/builtin/packages/perl-bio-perl/package.py b/var/spack/repos/builtin/packages/perl-bio-perl/package.py
new file mode 100644
index 0000000000..d67f96fd47
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-bio-perl/package.py
@@ -0,0 +1,71 @@
+##############################################################################
+# 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 *
+import inspect
+
+
+class PerlBioPerl(PerlPackage):
+    """Functional access to BioPerl for people who don't know objects"""
+
+    homepage = "http://search.cpan.org/~cjfields/BioPerl-1.007002/Bio/Perl.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz"
+
+    version('1.007002', 'a912c92b56d009198f1786b4cf560d5c')
+
+    depends_on('perl-module-build', type='build')
+    depends_on('perl-uri-escape', type=('build', 'run'))
+    depends_on('perl-io-string', type=('build', 'run'))
+    depends_on('perl-data-stag', type=('build', 'run'))
+    depends_on('perl-test-most', type=('build', 'run'))
+
+    def configure(self, spec, prefix):
+        # Overriding default configure method in order to cater to interactive
+        # Build.pl
+        self.build_method = 'Build.PL'
+        self.build_executable = Executable(
+            join_path(self.stage.source_path, 'Build'))
+
+        # Config questions consist of:
+        #    Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store
+        #        live database tests? y/n [n]
+        #
+        #    Install [a]ll BioPerl scripts, [n]one, or choose groups
+        #        [i]nteractively? [a]
+        #
+        #    Do you want to run tests that require connection to servers across
+        #        the internet (likely to cause some failures)? y/n [n]
+        #
+        # Eventually, someone can add capability for the other options, but
+        # the current answers are the most practical for a spack install.
+
+        config_answers = ['n\n', 'a\n', 'n\n']
+        config_answers_filename = 'spack-config.in'
+
+        with open(config_answers_filename, 'w') as f:
+            f.writelines(config_answers)
+
+        with open(config_answers_filename, 'r') as f:
+            inspect.getmodule(self).perl('Build.PL', '--install_base=%s' %
+                                         self.prefix, input=f)
diff --git a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py
new file mode 100644
index 0000000000..cda33ce84a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# 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 PerlClassDataInheritable(PerlPackage):
+    """For creating accessor/mutators to class data."""
+
+    homepage = "http://search.cpan.org/~tmtm/Class-Data-Inheritable-0.08/lib/Class/Data/Inheritable.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/T/TM/TMTM/Class-Data-Inheritable-0.08.tar.gz"
+
+    version('0.08', 'fc0fe65926eb8fb932743559feb54eb9')
diff --git a/var/spack/repos/builtin/packages/perl-data-stag/package.py b/var/spack/repos/builtin/packages/perl-data-stag/package.py
new file mode 100644
index 0000000000..136f7ad743
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-data-stag/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# 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 PerlDataStag(PerlPackage):
+    """Structured Tags datastructures"""
+
+    homepage = "http://search.cpan.org/~cmungall/Data-Stag-0.14/Data/Stag.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/Data-Stag-0.14.tar.gz"
+
+    version('0.14', 'f803acf74f1bfccc118aeac5483ee871')
+
+    depends_on('perl-io-string', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-exception-class/package.py b/var/spack/repos/builtin/packages/perl-exception-class/package.py
new file mode 100644
index 0000000000..262b7c7542
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-exception-class/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# 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 PerlExceptionClass(PerlPackage):
+    """A module that allows you to declare real exception classes in Perl"""
+
+    homepage = "http://search.cpan.org/~drolsky/Exception-Class-1.43/lib/Exception/Class.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/Exception-Class-1.43.tar.gz"
+
+    version('1.43', 'ff3fa5c26fa417b68d1f2d0a14cce7f1')
+
+    depends_on('perl-devel-stacktrace', type=('build', 'run'))
+    depends_on('perl-class-data-inheritable', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-io-string/package.py b/var/spack/repos/builtin/packages/perl-io-string/package.py
new file mode 100644
index 0000000000..eb595190ed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-string/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# 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 PerlIoString(PerlPackage):
+    """Emulate file interface for in-core strings"""
+
+    homepage = "http://search.cpan.org/~gaas/IO-String-1.08/String.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/IO-String-1.08.tar.gz"
+
+    version('1.08', '250e5424f290299fc3d6b5d1e9da3835')
diff --git a/var/spack/repos/builtin/packages/perl-test-deep/package.py b/var/spack/repos/builtin/packages/perl-test-deep/package.py
new file mode 100644
index 0000000000..83904d33cf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-test-deep/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# 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 PerlTestDeep(PerlPackage):
+    """Extremely flexible deep comparison"""
+
+    homepage = "http://search.cpan.org/~rjbs/Test-Deep-1.127/lib/Test/Deep.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Test-Deep-1.127.tar.gz"
+
+    version('1.127', 'eeafe5795ba20ba051a1423f4fa86dd6')
diff --git a/var/spack/repos/builtin/packages/perl-test-differences/package.py b/var/spack/repos/builtin/packages/perl-test-differences/package.py
new file mode 100644
index 0000000000..9a3653057f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-test-differences/package.py
@@ -0,0 +1,38 @@
+##############################################################################
+# 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 PerlTestDifferences(PerlPackage):
+    """Test strings and data structures and show differences if not ok"""
+
+    homepage = "http://search.cpan.org/~dcantrell/Test-Differences-0.64/lib/Test/Differences.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DC/DCANTRELL/Test-Differences-0.64.tar.gz"
+
+    version('0.64', 'ecfda620fe133e36a6e392d94ab8424d')
+
+    depends_on('perl-module-build', type='build')
+    depends_on('perl-capture-tiny', type=('build', 'run'))
+    depends_on('perl-text-diff', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-test-most/package.py b/var/spack/repos/builtin/packages/perl-test-most/package.py
new file mode 100644
index 0000000000..e4f78654da
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-test-most/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# 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 PerlTestMost(PerlPackage):
+    """Most commonly needed test functions and features."""
+
+    homepage = "http://search.cpan.org/~ovid/Test-Most-0.35/lib/Test/Most.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OV/OVID/Test-Most-0.35.tar.gz"
+
+    version('0.35', '03dbabd34d6f40af8bd47f5fbb0c6989')
+
+    depends_on('perl-exception-class', type=('build', 'run'))
+    depends_on('perl-test-differences', type=('build', 'run'))
+    depends_on('perl-test-exception', type=('build', 'run'))
+    depends_on('perl-test-warn', type=('build', 'run'))
+    depends_on('perl-test-deep', type=('build', 'run')) 
diff --git a/var/spack/repos/builtin/packages/perl-test-warn/package.py b/var/spack/repos/builtin/packages/perl-test-warn/package.py
new file mode 100644
index 0000000000..e924458c4c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-test-warn/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# 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 PerlTestWarn(PerlPackage):
+    """Perl extension to test methods for warnings"""
+
+    homepage = "http://search.cpan.org/~chorny/Test-Warn-0.30/Warn.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/C/CH/CHORNY/Test-Warn-0.30.tar.gz"
+
+    version('0.30', '8306b998a96d2cc69266b5248d550472')
diff --git a/var/spack/repos/builtin/packages/perl-text-diff/package.py b/var/spack/repos/builtin/packages/perl-text-diff/package.py
new file mode 100644
index 0000000000..0972c94fbd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-diff/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# 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 PerlTextDiff(PerlPackage):
+    """Provides a basic set of services akin to the GNU diff utility."""
+
+    homepage = "http://search.cpan.org/~neilb/Text-Diff-1.45/lib/Text/Diff.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/Text-Diff-1.45.tar.gz"
+
+    version('1.45', 'edf57b6189f7651a6be454062a4e6d9c')
+
+    depends_on('perl-algorithm-diff', type=('build', 'run'))