41 lines
1.4 KiB
Python
41 lines
1.4 KiB
Python
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Methyldackel(MakefilePackage):
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"""MethylDackel (formerly named PileOMeth, which was a temporary name
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derived due to it using a PILEup to extract METHylation metrics) will
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process a coordinate-sorted and indexed BAM or CRAM file containing
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some form of BS-seq alignments and extract per-base methylation
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metrics from them.
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"""
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homepage = "https://github.com/dpryan79/MethylDackel"
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url = "https://github.com/dpryan79/MethylDackel/archive/refs/tags/0.6.1.tar.gz"
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maintainers = ["snehring"]
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version("0.6.1", sha256="eeb1da4c830bcd9f3e6663a764947d957c41337643069524a4b545812fcf4819")
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depends_on("htslib@1.11:")
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depends_on("libbigwig")
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depends_on("curl")
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def edit(self, spec, prefix):
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filter_file(r"^prefix \?=.*$", "prefix = " + spec.prefix, "Makefile")
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filter_file(
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"$(LIBBIGWIG)",
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join_path(spec["libbigwig"].prefix.lib64, "libBigWig.a"),
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"Makefile",
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string=True,
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)
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filter_file(
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"-IlibBigWig",
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"-I" + spec["libbigwig"].prefix.include.libbigwig,
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"Makefile",
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string=True,
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)
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