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| author | Teague Sterling <teaguesterling@users.noreply.github.com> | 2024-09-10 10:45:59 -0700 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2024-09-10 11:45:59 -0600 |
| commit | decefe02344d2a2708e159d39fd1c5a39bfbfd14 (patch) | |
| tree | 5ba2dd52dd1eec9944dff88ded8ec041d8b4c148 /var | |
| parent | e2e5e74b9915fc553362c452d17f2d7c8714f2dc (diff) | |
| download | spack-decefe02344d2a2708e159d39fd1c5a39bfbfd14.tar.gz spack-decefe02344d2a2708e159d39fd1c5a39bfbfd14.tar.bz2 spack-decefe02344d2a2708e159d39fd1c5a39bfbfd14.tar.xz spack-decefe02344d2a2708e159d39fd1c5a39bfbfd14.zip | |
perl-bio-ensembl-io: new package (#44509)
* Adding the perl-bio-db-bigfile package
* Adding perl-bio-ensembl-io package
* 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>
* Rename package.py to package.py
* Update package.py
* Update package.py
* Removing unneeded dependencies
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Update package.py
* Update package.py
* Update package.py
* Update package.py
* Update package.py
* Updated from testing by @ebiarnie
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Updated from testing by @ebiarnie
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Fixing depends
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Fix styles
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
* Update package.py
---------
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/perl-bio-ensembl-io/package.py | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/perl-bio-ensembl-io/package.py b/var/spack/repos/builtin/packages/perl-bio-ensembl-io/package.py new file mode 100644 index 0000000000..5793e3bd51 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-bio-ensembl-io/package.py @@ -0,0 +1,47 @@ +# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack.package import * + + +class PerlBioEnsemblIo(Package): + """File parsing and writing code for Ensembl.""" + + homepage = "https://github.com/Ensembl/ensembl-io/" + url = "https://github.com/Ensembl/ensembl-io/archive/release/111.zip" + + maintainers("teaguesterling") + + license("APACHE-2.0", checked_by="teaguesterling") + + for vers, sha in [ + ("112", "ccbffe7c15318075463db46be348655a5914762e05ff47da2d72a4c99414d39a"), + ("111", "f81d4c1aea88aac7105aaa3fec548e39b79f129c7abc08b55be7d0345aa5482c"), + ("110", "83cf00ecdb6184be480fc3cbf0ffc322d3e9411e14602396fda8d153345d6c2e"), + ]: + version(vers, sha256=sha) + depends_on(f"perl-bio-ensembl@{vers}", when=f"@{vers}") + + extends("perl") + + variant("scripts", default=False, description="Install scripts") + + depends_on("perl-bio-bigfile") + depends_on("perl-bio-db-hts") + depends_on("perl-bio-ensembl") + depends_on("perl-bioperl@1.6.924") + depends_on("perl-compress-bzip2") + depends_on("perl-json") + depends_on("perl-try-tiny") + depends_on("perl-uri") + depends_on("vcftools") + + def install(self, spec, prefix): + install_tree("modules", prefix.lib.perl5) + mkdirp(prefix.share.ensembl) + for extra in ["scripts"]: + if spec.satisfies(f"+{extra}"): + extra = extra.replace("_", "-") + target = join_path(prefix.share.ensembl, extra) + install_tree(extra, target) |