diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/bcl2fastq2/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/bcl2fastq2/package.py | 47 |
1 files changed, 14 insertions, 33 deletions
diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py index 173bb050ff..f3eb3175ac 100644 --- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py +++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py @@ -1,30 +1,11 @@ -############################################################################## -# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. # -# 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/spack/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 -############################################################################## +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + from spack import * import os -import shutil +import glob import llnl.util.tty as tty @@ -36,8 +17,9 @@ class Bcl2fastq2(Package): call (BCL) files from a sequencing run into FASTQ files.""" - homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-18.html" + homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html" + version('2.20.0.422', '4dc99f1af208498b7279b66556329488') version('2.19.1.403', 'baba7a02767fd868e87cb36781d2be26') version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c') # 2.17.1.14 is no longer distributed. If you have a copy of the @@ -65,12 +47,11 @@ class Bcl2fastq2(Package): # v2.19.1.403 is only available via ftp. # who knows what the future will hold. def url_for_version(self, version): + url = "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip" if version.string == '2.19.1.403': - return "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v2.19.1-tar.zip" + return url.format(version.up_to(3).dotted) else: - url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip" - # - required to change the version from dots to dashes. - return url.format(version.dashed) + return url.format(version.up_to(3).dashed) # Illumina tucks the source inside a gzipped tarball inside a zip # file. We let the normal Spack expansion bit unzip the zip file, @@ -91,12 +72,12 @@ class Bcl2fastq2(Package): else: tty.msg("Unpacking bcl2fastq2 tarball") tty.msg("cwd sez: {0}".format(os.getcwd())) - tarball = 'bcl2fastq2-v{0}.tar.gz'.format( - self.version.dotted) - shutil.move(join_path('spack-expanded-archive', tarball), - '.') + tarball = glob.glob(join_path('spack-expanded-archive', + 'bcl2fastq2*.tar.gz'))[0] + copy(tarball, '.') os.rmdir('spack-expanded-archive') tar = which('tar') + tarball = os.path.basename(tarball) tar('-xf', tarball) tty.msg("Finished unpacking bcl2fastq2 tarball") return wrap |