d51af675ef
- [x] Replace `version(ver, checksum=None, **kwargs)` signature with
`version(ver, checksum=None, *, sha256=..., ...)` explicitly listing all arguments.
- [x] Fix various issues in packages:
- `tags` instead of `tag`
- `default` instead of `preferred`
- `sha26` instead of `sha256`
- etc
Also, use `sha256=...` consistently.
Note: setting `sha256` currently doesn't validate the checksum length, so you could do
`sha256="a"*32` and it would get checked as `md5`... but that's something for another PR.
35 lines
1.2 KiB
Python
35 lines
1.2 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 os
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from spack.package import *
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class SspaceLongread(Package):
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"""SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled
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contigs using long reads
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Note: A manual download is required for SSPACE-LongRead.
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Spack will search your current directory for the download file.
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Alternatively, add this file to a mirror so that Spack can find it.
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For instructions on how to set up a mirror, see
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https://spack.readthedocs.io/en/latest/mirrors.html"""
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homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread"
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manual_download = True
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version("1.1", md5="0bb5d8603d7ead4ff1596135a520cc26")
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depends_on("perl", type=("build", "run"))
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def url_for_version(self, version):
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return "file://{0}/40SSPACE-LongRead_v{1}.tar.gz".format(os.getcwd(), version.dashed)
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install("blasr", prefix.bin)
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install("SSPACE-LongRead.pl", prefix.bin)
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