
* Style: black 23, skip magic trailing commas * isort should use same line length as black * Fix unused import * Update version of black used in CI * Update new packages * Update new packages
106 lines
3.8 KiB
Python
106 lines
3.8 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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import glob
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from spack.package import *
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class Hisat2(MakefilePackage):
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"""HISAT2 is a fast and sensitive alignment program for mapping
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next-generation sequencing reads (whole-genome, transcriptome, and
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exome sequencing data) against the general human population (as well as
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against a single reference genome)."""
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homepage = "https://daehwankimlab.github.io/hisat2/"
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url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-source.zip"
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version(
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"2.2.1",
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sha256="48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1",
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url="https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download",
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extension="zip",
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)
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version(
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"2.2.0",
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sha256="0dd55168853b82c1b085f79ed793dd029db163773f52272d7eb51b3b5e4a4cdd",
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url="https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-source/download",
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extension="zip",
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)
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version("2.1.0", sha256="89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781")
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variant("sra", default=False, description="Add SRA (Sequence Read Archive) support")
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depends_on("perl", type="run")
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depends_on("python", type="run")
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depends_on("sra-tools", when="+sra")
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depends_on("ncbi-vdb", when="+sra")
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# patch to get SRA working
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patch("sra.patch", when="+sra")
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@when("+sra")
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def build(self, spec, prefix):
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make(
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"USE_SRA=1",
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"NCBI_NGS_DIR={0}".format(spec["sra-tools"].prefix),
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"NCBI_VDB_DIR={0}".format(spec["ncbi-vdb"].prefix),
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)
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def install(self, spec, prefix):
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if spec.satisfies("@:2.1.0"):
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install_tree("doc", prefix.doc)
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install_tree("example", prefix.example)
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install_tree("scripts", prefix.scripts)
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if "@:2.2.0" in spec:
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install_tree("hisatgenotype_modules", prefix.hisatgenotype_modules)
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install_tree("hisatgenotype_scripts", prefix.hisatgenotype_scripts)
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mkdirp(prefix.bin)
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install("hisat2", prefix.bin)
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install("hisat2-align-s", prefix.bin)
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install("hisat2-align-l", prefix.bin)
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install("hisat2-build", prefix.bin)
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install("hisat2-build-s", prefix.bin)
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install("hisat2-build-l", prefix.bin)
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install("hisat2-inspect", prefix.bin)
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install("hisat2-inspect-s", prefix.bin)
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install("hisat2-inspect-l", prefix.bin)
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install("*.py", prefix.bin)
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if "@2.2:" in spec:
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install("hisat2-repeat", prefix.bin)
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@run_after("install")
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def filter_sbang(self):
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with working_dir(self.prefix.bin):
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pattern = "^#!.*/usr/bin/env python"
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repl = "#!{0}".format(self.spec["python"].command.path)
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files = ["hisat2-build", "hisat2-inspect"]
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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pattern = "^#!.*/usr/bin/env perl"
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repl = "#!{0}".format(self.spec["perl"].command.path)
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files = ["hisat2"]
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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pattern = "^#!.*/usr/bin/env python3"
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repl = "#!{0}".format(self.spec["python"].command.path)
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files = glob.glob("*.py")
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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with working_dir(self.prefix.scripts):
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pattern = "^#!.*/usr/bin/perl"
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repl = "#!{0}".format(self.spec["perl"].command.path)
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files = glob.glob("*.pl")
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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