833f1de24a
When PR #26659 is merged, boost version boost@1.54.0 will be available for build too. Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
106 lines
4.2 KiB
Python
106 lines
4.2 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import glob
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import os
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import llnl.util.tty as tty
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from spack import *
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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', sha256='8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3')
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version('2.19.1.403', sha256='cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806')
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conflicts('platform=darwin',
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msg='malloc.h/etc requirements break build on macs')
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depends_on('boost@1.54.0:1.55')
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depends_on('cmake@2.8.9:', type='build')
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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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# The tarfile should now reside in the well-known source
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# directory (i.e., self.stage.source_path).
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with working_dir(self.stage.path):
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source_subdir = os.path.relpath(self.stage.source_path,
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self.stage.path)
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files = glob.glob(os.path.join(source_subdir,
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'bcl2fastq2*.tar.gz'))
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if len(files) == 1:
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# Rename the tarball so it resides in self.stage.path
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# alongside the original zip file before unpacking it.
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tarball = files[0]
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basename = os.path.basename(tarball)
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os.rename(tarball, basename)
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tty.msg("Unpacking bcl2fastq2 tarball")
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tar = which('tar')
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tar('-xf', basename)
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# Rename the unpacked directory to the well-known
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# source path self.stage.source_path.
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os.rename('bcl2fastq', source_subdir)
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tty.msg("Finished unpacking bcl2fastq2 tarball")
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elif self.stage.expanded:
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# The unpacked files already reside in the "well known"
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# source directory (i.e., self.stage.source_path).
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tty.msg("The tarball has already been unpacked.")
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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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