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# Copyright 2013-2021 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)
import glob
import os
import llnl.util.tty as tty
from spack import *
# 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', sha256='8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3')
version('2.19.1.403', sha256='cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806')
conflicts('platform=darwin',
msg='malloc.h/etc requirements break build on macs')
depends_on('boost@1.54.0')
depends_on('cmake@2.8.9:', type='build')
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()
# The tarfile should now reside in the well-known source
# directory (i.e., self.stage.source_path).
with working_dir(self.stage.path):
source_subdir = os.path.relpath(self.stage.source_path,
self.stage.path)
files = glob.glob(os.path.join(source_subdir,
'bcl2fastq2*.tar.gz'))
if len(files) == 1:
# Rename the tarball so it resides in self.stage.path
# alongside the original zip file before unpacking it.
tarball = files[0]
basename = os.path.basename(tarball)
os.rename(tarball, basename)
tty.msg("Unpacking bcl2fastq2 tarball")
tar = which('tar')
tar('-xf', basename)
# Rename the unpacked directory to the well-known
# source path self.stage.source_path.
os.rename('bcl2fastq', source_subdir)
tty.msg("Finished unpacking bcl2fastq2 tarball")
elif self.stage.expanded:
# The unpacked files already reside in the "well known"
# source directory (i.e., self.stage.source_path).
tty.msg("The tarball has already been unpacked.")
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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