fastq-screen: new package (#5431)

* fastq-screen: new package

* fixing descriptions and previously made packages' old copyright date

* added wrong perl package after change

6 files changed, 228 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/fastq-screen/package.py b/var/spack/repos/builtin/packages/fastq-screen/package.py
new file mode 100644
index 0000000000..63aa2d3907
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fastq-screen/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# 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 FastqScreen(Package):
+    """FastQ Screen allows you to screen a library of sequences in FastQ format
+       against a set of sequence databases so you can see if the composition of
+       the library matches with what you expect."""
+
+    homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
+    url      = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.11.2.tar.gz"
+
+    version('0.11.2', 'ef79f16ee553aaa0ab2fc14ea11e5473')
+
+    depends_on('perl', type='run')
+    depends_on('perl-gd-graph', type='run')
+    depends_on('bowtie')
+    depends_on('bowtie2')
+    depends_on('bwa')
+    depends_on('samtools')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py
new file mode 100644
index 0000000000..dbd584ca95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-capture-tiny/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 PerlCaptureTiny(PerlPackage):
+    """Capture STDOUT and STDERR from Perl, XS or external programs"""
+
+    homepage = "http://search.cpan.org/~dagolden/Capture-Tiny-0.46/lib/Capture/Tiny.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/Capture-Tiny-0.46.tar.gz"
+
+    version('0.46', 'd718af07729d26a793949ca6ba2580a7')
diff --git a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py
new file mode 100644
index 0000000000..fcc76d183c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/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 PerlExtutilsPkgconfig(PerlPackage):
+    """simplistic interface to pkg-config"""
+
+    homepage = "http://search.cpan.org/~xaoc/ExtUtils-PkgConfig-1.16/lib/ExtUtils/PkgConfig.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz"
+
+    version('1.16', 'b86318f2b6ac6af3ee985299e1e38fe5')
diff --git a/var/spack/repos/builtin/packages/perl-gd-graph/package.py b/var/spack/repos/builtin/packages/perl-gd-graph/package.py
new file mode 100644
index 0000000000..7d3e9c7d0f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-gd-graph/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# 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 PerlGdGraph(PerlPackage):
+    """Graph Plotting Module for Perl 5"""
+
+    homepage = "http://search.cpan.org/~bwarfield/GDGraph/Graph.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/B/BW/BWARFIELD/GDGraph-1.44.tar.gz"
+
+    version('1.4308', 'fcdd34d5e09ae917b5d264887734b3b1')
+
+    depends_on('perl-capture-tiny', type=('build', 'run'))
+    depends_on('perl-test-exception', type=('build', 'run'))
+    depends_on('perl-gd-text', type=('build', 'run'))
+    depends_on('perl-gd', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-gd-text/package.py b/var/spack/repos/builtin/packages/perl-gd-text/package.py
new file mode 100644
index 0000000000..fd824092f3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-gd-text/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 PerlGdText(PerlPackage):
+    """Text utilities for use with GD"""
+
+    homepage = "http://search.cpan.org/~mverb/GDTextUtil-0.86/Text.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MV/MVERB/GDTextUtil-0.86.tar.gz"
+
+    version('0.86', '941ad06eadc86b47f3a32da405665c41')
+
+    depends_on('perl-gd', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-gd/package.py b/var/spack/repos/builtin/packages/perl-gd/package.py
new file mode 100644
index 0000000000..209a82a88c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-gd/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# 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 PerlGd(PerlPackage):
+    """Interface to Gd Graphics Library"""
+
+    homepage = "http://search.cpan.org/~lds/GD-2.53/GD.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GD-2.53.tar.gz"
+
+    version('2.53', 'd2c9b18123bcaff8672eb50f2eb37ed3')
+
+    depends_on('perl-module-build', type='build')
+    depends_on('perl-extutils-makemaker', type=('build', 'run'))
+    depends_on('perl-extutils-pkgconfig', type=('build', 'run'))
+    depends_on('libgd')