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sabre (#4619)

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* sabre initial commit, works but test does not

* removing test until I have time to fix it

* sabre: fixing flake8 errors

* sabre: changing to MakefilePackage
This commit is contained in:
Levi Baber 2017-07-02 06:31:17 -07:00 committed by Adam J. Stewart
parent f6e2320ef0
commit 245eee7a56
1 changed files with 48 additions and 0 deletions
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var/spack/repos/builtin/packages/sabre/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 Sabre(MakefilePackage):
"""Sabre is a tool that will demultiplex barcoded reads into separate
files. It will work on both single-end and paired-end data in fastq
format. It simply compares the provided barcodes with each read and
separates the read into its appropriate barcode file, after stripping
the barcode from the read (and also stripping the quality values of
the barcode bases). If a read does not have a recognized barcode,
then it is put into the unknown file.
"""
homepage = "https://github.com/najoshi/sabre"
url = "https://github.com/najoshi/sabre"
version('2013-09-27', git='https://github.com/najoshi/sabre.git', commit='039a55e500ba07b7e6432ea6ec2ddcfb3471d949')
depends_on('zlib')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('sabre', prefix.bin)