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.
54 lines
2.1 KiB
Python
54 lines
2.1 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 Supernova(Package):
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"""Supernova is a software package for de novo assembly from Chromium
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Linked-Reads that are made from a single whole-genome library from an
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individual DNA source.
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A key feature of Supernova is that it creates diploid assemblies, thus
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separately representing maternal and paternal chromosomes over very long
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distances. Almost all other methods instead merge homologous chromosomes
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into single incorrect 'consensus' sequences. Supernova is the only
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practical method for creating diploid assemblies of large genomes.
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To install this package, you will need to go to the supernova download
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page of supernova, register with your email address and download
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supernova yourself. Spack will search your current directory for the
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download file. Alternatively, add this file yo a mirror so that Spack
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can find it. 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://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome"
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manual_download = True
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version("2.1.1", sha256="2f58eb66951e257b89359134ab8e35ad638c4ed51cb3fb8121625dfcc7761938")
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version("2.0.1", md5="3697ce043c798fcb672fe0a66c56d6f0")
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depends_on("bcl2fastq2")
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def url_for_version(self, version):
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return "file://{0}/supernova-{1}.tar.gz".format(os.getcwd(), version)
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def setup_run_environment(self, env):
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env.prepend_path("PATH", self.prefix)
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def install(self, spec, prefix):
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rm = which("rm")
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# remove the broken symlinks
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if os.path.isdir("anaconda-cs/2.2.0-anaconda-cs-c7/lib"):
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rm(
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"anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtcl.so",
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"anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtk.so",
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)
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install_tree(".", prefix)
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