1c528719cb
* Adding the perl-bio-db-bigfile package
* Adding perl-bio-ensembl-variation package
* Adding perl-bio-ensembl-io package
* Update package.py
* Update package.py
* Update package.py
* Update package.py
* Update package.py
* Updating dependent package handling
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Updating dependent package handling
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Reverting variants
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Update package.py
* Rename package.py to package.py
* Update package.py
* Update package.py
* Update package.py
* Fix variant installation and dependencies
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Styles
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Removing unneeded dependencies
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Update package.py
* Update package.py
* Update package.py
* perl-bio-ensembl: update sha256 of 112
* perl-bio-ensembl-variation: add perl-bio-ensembl-funcgen@{vers}
---------
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
47 lines
1.7 KiB
Python
47 lines
1.7 KiB
Python
# Copyright 2013-2024 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 PerlBioEnsembl(Package):
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"""The Ensembl Core Perl API and SQL schema"""
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homepage = "https://useast.ensembl.org/info/docs/api/index.html"
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url = "https://github.com/Ensembl/ensembl/archive/release/111.zip"
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def url_for_version(self, version):
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return f"https://github.com/Ensembl/ensembl/archive/release/{version.up_to(1)}.zip"
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maintainers("teaguesterling")
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license("APACHE-2.0", checked_by="teaguesterling")
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version("112", sha256="7c2c5265abe74b462cd4f8b26f140a4c4945cd0e2971f40711afbb4b38db5997")
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version("111", sha256="346c47c75a6fa8dcfd9f9d22e9f1e0ccc35b2fb99f75980a0c74d892e4ab2b6d")
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version("110", sha256="fdf725cad1a980ddf900f1af1a72bf1de355f15e408664930ed84aeccfefad15")
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extends("perl")
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variant("sql", default=False, description="Install SQL files")
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variant("misc_scripts", default=False, description="Install misc Ensembl scripts")
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depends_on("perl-dbi")
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depends_on("perl-dbd-mysql@:4")
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depends_on("perl-http-tiny")
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depends_on("perl-io-compress")
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depends_on("perl-uri")
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depends_on("perl-config-inifiles")
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depends_on("perl-gzip-faster")
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depends_on("perl-list-moreutils")
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def install(self, spec, prefix):
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install_tree("modules", prefix.lib.perl5)
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mkdirp(prefix.share.ensembl)
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for extra in ["sql", "misc_scripts"]:
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if spec.satisfies(f"+{extra}"):
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extra = extra.replace("_", "-")
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target = join_path(prefix.share.ensembl, extra)
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install_tree(extra, target)
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