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perl-bio-ensembl-variation: new package (#44507)

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* 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>
This commit is contained in:
Teague Sterling 2024-10-02 07:21:06 -07:00 committed by GitHub
parent f3faeb0f77
commit 1c528719cb
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2 changed files with 89 additions and 1 deletions
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88
var/spack/repos/builtin/packages/perl-bio-ensembl-variation/package.py Normal file
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@ -0,0 +1,88 @@
# 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 PerlBioEnsemblVariation(Package):
"""The Ensembl Variation Perl API and SQL schema."""
homepage = "http://www.ensembl.org/info/docs/api/variation/"
url = "https://github.com/Ensembl/ensembl-variation/archive/release/112.zip"
maintainers("teaguesterling")
license("APACHE-2.0", checked_by="teaguesterling")
for vers, sha in [
("112", "ad75ff0a9efbf2d5c10ab5087d414bac685819664d01fbe4a9765393bd742a7c"),
("111", "b2171b3f5f82a2b7e849c0ec8dc254f4bace4b3faba1b3ab75c5eea596e33bef"),
("110", "210d627dcb867d9fda3a0d94428da256f394c32e34df5171b9b9e604507e1f05"),
]:
version(vers, sha256=sha)
depends_on(f"perl-bio-ensembl@{vers}", when=f"@{vers}")
depends_on(f"perl-bio-ensembl-io@{vers}", when=f"@{vers}+tools", type="run")
depends_on(f"perl-bio-ensembl-funcgen@{vers}", when=f"@{vers}", type="run")
extends("perl")
variant("sql", default=False, description="Install SQL files")
variant("schema", default=False, description="Install schema documentation")
variant("nextflow", default=False, description="Install nextflow workflows")
variant("scripts", default=False, description="Install additional scripts")
variant("tools", default=False, description="Install additional tools")
variant("ld", default=False, description="Compile LD calculation tools")
depends_on("perl-bioperl@1.6.924")
depends_on("perl-bio-bigfile")
depends_on("perl-bio-db-hts")
depends_on("perl-sereal")
depends_on("perl-json")
depends_on("perl-set-intervaltree")
depends_on("perl-string-approx")
depends_on("perl-xml-hash-xs")
depends_on("perl-xml-libxml")
depends_on("perl-date-manip")
with when("+ld"):
depends_on("htslib", type="build")
depends_on("gmake", type="build")
phases = ("build", "install")
def setup_build_environment(self, env):
if self.spec.satisfies("+ld"):
env.set("HTSLIB_DIR", self.spec["htslib"].prefix.include)
def build(self, spec, prefix):
if spec.satisfies("+ld"):
make = which("make")
with working_dir("C_code"):
make()
if spec.satisfies("+tools"):
# Fix the fact that phenotype_annotation isn't executable
chmod = which("chmod")
chmod("+x", "tools/phenotype_annotation/phenotype_annotation")
def install(self, spec, prefix):
install_tree("modules", prefix.lib.perl5)
mkdirp(prefix.share.ensembl.variation)
for extra in ["sql", "schema", "nextflow", "scripts"]:
if spec.satisfies(f"+{extra}"):
target = join_path(prefix.share.ensembl, extra)
install_tree(extra, target)
for requested, targets in {
"+ld": ["C_code/calc_genotypes", "C_code/ld_vcf"],
"+tools": [
"tools/linkage_disequilibrium/ld_tool",
"tools/variant_simulator/simulate_variation",
"tools/phenotype_annotation/phenotype_annotation",
],
}.items():
if spec.satisfies(requested):
mkdirp(prefix.bin)
for target in targets:
install(target, prefix.bin)

2
var/spack/repos/builtin/packages/perl-bio-ensembl/package.py
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@ -18,7 +18,7 @@ def url_for_version(self, version):
license("APACHE-2.0", checked_by="teaguesterling")
version("112", sha256="8a6b46840df71c4332d2de6027596ed4417a26111800d7ff0636199363568235")
version("112", sha256="7c2c5265abe74b462cd4f8b26f140a4c4945cd0e2971f40711afbb4b38db5997")
version("111", sha256="346c47c75a6fa8dcfd9f9d22e9f1e0ccc35b2fb99f75980a0c74d892e4ab2b6d")
version("110", sha256="fdf725cad1a980ddf900f1af1a72bf1de355f15e408664930ed84aeccfefad15")