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Added STAR-Fusion (#4380)

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* added perl-star-fusion and perl-intervaltree

* added perl-star-fusion and all dependencies

* changes

* made changes as requested to perl-star-fusion dependencies

* changed perl-intervaltree dependency

* changes to star fusion

* now using perl properly
This commit is contained in:
Douglas Duckworth 2017-06-27 14:53:58 -04:00 committed by Adam J. Stewart
parent 77218b1c8d
commit 7b0d295a4c
4 changed files with 176 additions and 0 deletions
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41
var/spack/repos/builtin/packages/perl-dbfile/package.py Normal file
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##############################################################################
# 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')

37
var/spack/repos/builtin/packages/perl-intervaltree/package.py Normal file
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##############################################################################
# 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')

59
var/spack/repos/builtin/packages/perl-star-fusion/package.py Normal file
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##############################################################################
# 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)

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var/spack/repos/builtin/packages/perl-uri-escape/package.py Normal file
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##############################################################################
# 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')