247f24e015
* bcl2fastq2: package update * package/bcl2fastq2: homepage fix * package/bcl2fastq2: glob fix * package/bcl2fastq2: code clean up * package/bcl2fastq2: code clean up #2
112 lines
4.7 KiB
Python
112 lines
4.7 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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import os
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import shutil
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import glob
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import llnl.util.tty as tty
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# This application uses cmake to build, but they wrap it with a
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# configure script that performs dark magic. This package does it
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# their way.
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class Bcl2fastq2(Package):
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"""The bcl2fastq2 Conversion Software converts base
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call (BCL) files from a sequencing run into FASTQ
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files."""
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homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html"
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version('2.20.0.422', '4dc99f1af208498b7279b66556329488')
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version('2.19.1.403', 'baba7a02767fd868e87cb36781d2be26')
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version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c')
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# 2.17.1.14 is no longer distributed. If you have a copy of the
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# source tarball, you can drop it into a local mirror w/ the name
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# mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
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version('2.17.1.14', '7426226c6db095862e636b95c38608d3')
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depends_on('boost@1.54.0')
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depends_on('cmake@2.8.9:')
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depends_on('libxml2@2.7.8')
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depends_on('libxslt@1.1.26~crypto')
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depends_on('libgcrypt')
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depends_on('zlib')
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# Their cmake macros don't set the flag when they find a library
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# that makes them happy.
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patch('cmake-macros.patch')
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# After finding the libxslt bits, cmake still needs to wire in the
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# libexslt bits.
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patch('cxxConfigure-cmake.patch')
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root_cmakelists_dir = 'src'
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# v2.17.1.14 and v2.18.0.12 were available via HTTP.
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# v2.19.1.403 is only available via ftp.
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# who knows what the future will hold.
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def url_for_version(self, version):
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url = "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
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if version.string == '2.19.1.403':
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return url.format(version.up_to(3).dotted)
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else:
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return url.format(version.up_to(3).dashed)
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# Illumina tucks the source inside a gzipped tarball inside a zip
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# file. We let the normal Spack expansion bit unzip the zip file,
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# then follow it with a function untars the tarball after Spack's
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# done it's bit.
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def do_stage(self, mirror_only=False):
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# wrap (decorate) the standard expand_archive step with a
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# helper, then call the real do_stage().
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self.stage.expand_archive = self.unpack_it(self.stage.expand_archive)
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super(Bcl2fastq2, self).do_stage(mirror_only)
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def unpack_it(self, f):
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def wrap():
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f() # call the original expand_archive()
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with working_dir(self.stage.path):
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if os.path.isdir('bcl2fastq'):
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tty.msg("The tarball has already been unpacked")
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else:
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tty.msg("Unpacking bcl2fastq2 tarball")
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tty.msg("cwd sez: {0}".format(os.getcwd()))
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tarball = glob.glob(join_path('spack-expanded-archive',
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'bcl2fastq2*.tar.gz'))[0]
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shutil.move(tarball, '.')
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os.rmdir('spack-expanded-archive')
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tar = which('tar')
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tarball = os.path.basename(tarball)
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tar('-xf', tarball)
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tty.msg("Finished unpacking bcl2fastq2 tarball")
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return wrap
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def install(self, spec, prefix):
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bash = which('bash')
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bash("src/configure", "--prefix={0}".format(prefix),
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"--with-cmake={0}".format(join_path(spec['cmake'].prefix.bin,
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"cmake")))
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make()
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make("install")
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