perl-bio-ensembl: new package (#44506)

* Adding perl-bio-ensembl package

* Fixing checksums

* Update package.py

1 files changed, 46 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/perl-bio-ensembl/package.py b/var/spack/repos/builtin/packages/perl-bio-ensembl/package.py
new file mode 100644
index 0000000000..763c75e91d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-bio-ensembl/package.py
@@ -0,0 +1,46 @@
+# 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 PerlBioEnsembl(Package):
+    """The Ensembl Core Perl API and SQL schema"""
+
+    homepage = "https://useast.ensembl.org/info/docs/api/index.html"
+    url = "https://github.com/Ensembl/ensembl/archive/release/111.zip"
+
+    def url_for_version(self, version):
+        return f"https://github.com/Ensembl/ensembl/archive/release/{version.up_to(1)}.zip"
+
+    maintainers("teaguesterling")
+
+    license("APACHE-2.0", checked_by="teaguesterling")
+
+    version("112", sha256="8a6b46840df71c4332d2de6027596ed4417a26111800d7ff0636199363568235")
+    version("111", sha256="346c47c75a6fa8dcfd9f9d22e9f1e0ccc35b2fb99f75980a0c74d892e4ab2b6d")
+    version("110", sha256="fdf725cad1a980ddf900f1af1a72bf1de355f15e408664930ed84aeccfefad15")
+
+    extends("perl")
+
+    variant("sql", default=False, description="Install SQL files")
+    variant("misc_scripts", default=False, description="Install misc Ensembl scripts")
+
+    depends_on("perl-dbi")
+    depends_on("perl-dbd-mysql@:4")
+    depends_on("perl-http-tiny")
+    depends_on("perl-io-compress")
+    depends_on("perl-uri")
+    depends_on("perl-config-inifiles")
+    depends_on("perl-gzip-faster")
+    depends_on("perl-list-moreutils")
+
+    def install(self, spec, prefix):
+        install_tree("modules", prefix.lib.perl5)
+        mkdirp(prefix.share.ensembl)
+        for extra in ["sql", "misc_scripts"]:
+            if spec.satisfies(f"+{extra}"):
+                extra = extra.replace("_", "-")
+                target = join_path(prefix.share.ensembl, extra)
+                install_tree(extra, target)