diff options
4 files changed, 176 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-dbfile/package.py new file mode 100644 index 0000000000..7445d6e63a --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-dbfile/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 PerlDbfile(PerlPackage): + """DB_File is a module which allows Perl programs to make use of the + facilities provided by Berkeley DB version 1.x (if you have a newer version + of DB, see "Using DB_File with Berkeley DB version 2 or greater"). + It is assumed that you have a copy of the Berkeley DB manual pages at hand + when reading this documentation. The interface defined here mirrors the + Berkeley DB interface closely.""" + + homepage = "https://metacpan.org/pod/DB_File" + url = "https://cpan.metacpan.org/authors/id/P/PM/PMQS/DB_File-1.840.tar.gz" + + version('1.840', '8a2e98d457a216840ac893913c24141e') + + depends_on('perl-extutils-makemaker', type='build') diff --git a/var/spack/repos/builtin/packages/perl-intervaltree/package.py b/var/spack/repos/builtin/packages/perl-intervaltree/package.py new file mode 100644 index 0000000000..bcf1204c53 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-intervaltree/package.py @@ -0,0 +1,37 @@ +############################################################################## +# 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 PerlIntervaltree(PerlPackage): + """Set::IntervalTree uses Interval Trees to store and efficiently look up + ranges using a range-based lookup.""" + + homepage = "https://metacpan.org/release/Set-IntervalTree" + url = "https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/Set-IntervalTree-0.10.tar.gz" + + version('0.10', '42efe9369f1b30e7fd04e10c07226b06') + + depends_on('perl-extutils-makemaker', type='build') diff --git a/var/spack/repos/builtin/packages/perl-star-fusion/package.py b/var/spack/repos/builtin/packages/perl-star-fusion/package.py new file mode 100644 index 0000000000..65d673bf3b --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-star-fusion/package.py @@ -0,0 +1,59 @@ +############################################################################## +# 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 * +from glob import glob + + +class PerlStarFusion(Package): + """STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis + Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate + fusion transcripts supported by Illumina reads. STAR-Fusion further + processes the output generated by the STAR aligner to map junction reads + and spanning reads to a reference annotation set.""" + + homepage = "https://github.com/STAR-Fusion/STAR-Fusion" + url = "https://github.com/STAR-Fusion/STAR-Fusion.git" + + version('master', git='https://github.com/STAR-Fusion/STAR-Fusion.git', commit='a16a0a8') + + extends('perl') + + depends_on('star', type=('build', 'run')) + depends_on('perl', type=('build', 'run')) + depends_on('perl-intervaltree', type=('build', 'run')) + depends_on('perl-dbi', type=('build', 'run')) + depends_on('perl-dbfile', type=('build', 'run')) + depends_on('perl-uri-escape', type=('build', 'run')) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('STAR-Fusion', prefix.bin) + mkdirp(perl_lib_dir) + with working_dir('PerlLib'): + for pm in glob("*.pm"): + install(pm, perl_lib_dir) + with working_dir('util'): + for files in glob("*"): + install(files, prefix.bin) diff --git a/var/spack/repos/builtin/packages/perl-uri-escape/package.py b/var/spack/repos/builtin/packages/perl-uri-escape/package.py new file mode 100644 index 0000000000..ffeb06f979 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-uri-escape/package.py @@ -0,0 +1,39 @@ +############################################################################## +# 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 PerlUriEscape(PerlPackage): + """This module provides functions to percent-encode and percent-decode URI + strings as defined by RFC 3986. Percent-encoding URI's is informally called + "URI escaping". This is the terminology used by this module, which predates + the formalization of the terms by the RFC by several years.""" + + homepage = "https://metacpan.org/pod/URI::Escape" + url = "https://cpan.metacpan.org/authors/id/E/ET/ETHER/URI-1.71.tar.gz" + + version('1.71', '247c3da29a794f72730e01aa5a715daf') + + depends_on('perl-extutils-makemaker', type='build') |