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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 os
from spack.package import *
class EaUtils(MakefilePackage):
"""Command-line tools for processing biological sequencing data. Barcode
demultiplexing, adapter trimming, etc. Primarily written to support an
Illumina based pipeline - but should work with any FASTQs."""
homepage = "https://expressionanalysis.github.io/ea-utils/"
url = "https://github.com/ExpressionAnalysis/ea-utils/archive/1.04.807.tar.gz"
git = "https://github.com/ExpressionAnalysis/ea-utils.git"
maintainers("snehring")
version("2021-10-20", commit="10c21926a4dce4289d5052acfd73b8e744d4fede")
version(
"1.04.807",
sha256="aa09d25e6aa7ae71d2ce4198a98e58d563f151f8ff248e4602fa437f12b8d05f",
deprecated=True,
)
depends_on("sparsehash")
depends_on("zlib-api")
depends_on("gsl")
depends_on("bamtools")
depends_on("perl", type=["build", "run"])
build_directory = "clipper"
def edit(self, spec, prefix):
with working_dir(self.build_directory):
filter_file("/usr", prefix, "Makefile")
# remove tests from all rule
filter_file(r"^all:.*$", "all: $(BIN)", "Makefile")
# remove the vendored sparsehash
filter_file(" sparsehash", "", "Makefile")
# replace system perl references
for f in next(os.walk(os.getcwd()))[2]:
filter_file("/usr/bin/perl", spec["perl"].prefix.bin.perl, f)
# fix up test script require path
tests = ["join.t", "mcf.t", "multx.t"]
rep = 'require "{0}";'.format(os.path.join(os.getcwd(), "t", "test-prep.pl"))
for f in tests:
filter_file(r"^require.*$", rep, os.path.join(os.getcwd(), "t", f))
def flag_handler(self, name, flags):
if name.lower() == "cxxflags":
flags.append(self.compiler.cxx11_flag)
return (flags, None, None)
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