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

* 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>

2 files changed, 89 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/perl-bio-ensembl-variation/package.py b/var/spack/repos/builtin/packages/perl-bio-ensembl-variation/package.py
new file mode 100644
index 0000000000..0078c28061
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-bio-ensembl-variation/package.py
@@ -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)
diff --git a/var/spack/repos/builtin/packages/perl-bio-ensembl/package.py b/var/spack/repos/builtin/packages/perl-bio-ensembl/package.py
index 763c75e91d..8cf860e3d7 100644
--- a/var/spack/repos/builtin/packages/perl-bio-ensembl/package.py
+++ b/var/spack/repos/builtin/packages/perl-bio-ensembl/package.py
@@ -18,7 +18,7 @@ class PerlBioEnsembl(Package):
 
     license("APACHE-2.0", checked_by="teaguesterling")
 
-    version("112", sha256="8a6b46840df71c4332d2de6027596ed4417a26111800d7ff0636199363568235")
+    version("112", sha256="7c2c5265abe74b462cd4f8b26f140a4c4945cd0e2971f40711afbb4b38db5997")
     version("111", sha256="346c47c75a6fa8dcfd9f9d22e9f1e0ccc35b2fb99f75980a0c74d892e4ab2b6d")
     version("110", sha256="fdf725cad1a980ddf900f1af1a72bf1de355f15e408664930ed84aeccfefad15")