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authorAudrey Thoma <las_thoma15@iastate.edu>2017-09-28 13:48:31 -0500
committerChristoph Junghans <christoph.junghans@gmail.com>2017-09-28 12:48:31 -0600
commit3f44eb01795e7f8b98e01b7abfc7c582fe6edabf (patch)
tree89e233ecac099d8f591cf41518aa84a513ffb48e
parent0ce93d733303797c366b49df177e64a61d324208 (diff)
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fastq-screen: new package (#5431)
* fastq-screen: new package * fixing descriptions and previously made packages' old copyright date * added wrong perl package after change
-rw-r--r--var/spack/repos/builtin/packages/fastq-screen/package.py46
-rw-r--r--var/spack/repos/builtin/packages/perl-capture-tiny/package.py34
-rw-r--r--var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py34
-rw-r--r--var/spack/repos/builtin/packages/perl-gd-graph/package.py39
-rw-r--r--var/spack/repos/builtin/packages/perl-gd-text/package.py36
-rw-r--r--var/spack/repos/builtin/packages/perl-gd/package.py39
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')