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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
import glob
import llnl.util.tty as tty
# This application uses cmake to build, but they wrap it with a
# configure script that performs dark magic. This package does it
# their way.
class Bcl2fastq2(Package):
"""The bcl2fastq2 Conversion Software converts base
call (BCL) files from a sequencing run into FASTQ
files."""
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
# source tarball, you can drop it into a local mirror w/ the name
# mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
version('2.17.1.14', '7426226c6db095862e636b95c38608d3')
depends_on('boost@1.54.0')
depends_on('cmake@2.8.9:')
depends_on('libxml2@2.7.8')
depends_on('libxslt@1.1.26~crypto')
depends_on('libgcrypt')
depends_on('zlib')
# Their cmake macros don't set the flag when they find a library
# that makes them happy.
patch('cmake-macros.patch')
# After finding the libxslt bits, cmake still needs to wire in the
# libexslt bits.
patch('cxxConfigure-cmake.patch')
root_cmakelists_dir = 'src'
# v2.17.1.14 and v2.18.0.12 were available via HTTP.
# 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 url.format(version.up_to(3).dotted)
else:
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,
# then follow it with a function untars the tarball after Spack's
# done it's bit.
def do_stage(self, mirror_only=False):
# wrap (decorate) the standard expand_archive step with a
# helper, then call the real do_stage().
self.stage.expand_archive = self.unpack_it(self.stage.expand_archive)
super(Bcl2fastq2, self).do_stage(mirror_only)
def unpack_it(self, f):
def wrap():
f() # call the original expand_archive()
with working_dir(self.stage.path):
if os.path.isdir('bcl2fastq'):
tty.msg("The tarball has already been unpacked")
else:
tty.msg("Unpacking bcl2fastq2 tarball")
tty.msg("cwd sez: {0}".format(os.getcwd()))
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
def install(self, spec, prefix):
bash = which('bash')
bash("src/configure", "--prefix={0}".format(prefix),
"--with-cmake={0}".format(join_path(spec['cmake'].prefix.bin,
"cmake")))
make()
make("install")
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