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# Copyright 2013-2023 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.package import *
from spack.pkg.builtin.boost import Boost
# 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@1.54.0:1.55")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
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-api")
# 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")
# -msse2 isn't valid for arm
patch("cxxConfigure-aarch64.patch", when="target=aarch64:")
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().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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