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# Copyright 2013-2024 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.package import *
class Methyldackel(MakefilePackage):
"""MethylDackel (formerly named PileOMeth, which was a temporary name
derived due to it using a PILEup to extract METHylation metrics) will
process a coordinate-sorted and indexed BAM or CRAM file containing
some form of BS-seq alignments and extract per-base methylation
metrics from them.
"""
homepage = "https://github.com/dpryan79/MethylDackel"
url = "https://github.com/dpryan79/MethylDackel/archive/refs/tags/0.6.1.tar.gz"
maintainers("snehring")
license("MIT")
version("0.6.1", sha256="eeb1da4c830bcd9f3e6663a764947d957c41337643069524a4b545812fcf4819")
depends_on("htslib@1.11:")
depends_on("libbigwig")
depends_on("curl")
def edit(self, spec, prefix):
filter_file(r"^prefix \?=.*$", "prefix = " + spec.prefix, "Makefile")
filter_file(
"$(LIBBIGWIG)",
join_path(spec["libbigwig"].prefix.lib64, "libBigWig.a"),
"Makefile",
string=True,
)
filter_file(
"-IlibBigWig",
"-I" + spec["libbigwig"].prefix.include.libbigwig,
"Makefile",
string=True,
)
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