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>
2024-09-10 10:45:59 -07:00 · 2024-09-10 10:45:59 -07:00 · decefe0234
commit decefe0234
parent e2e5e74b99
1 changed files with 47 additions and 0 deletions
--- a/var/spack/repos/builtin/packages/perl-bio-ensembl-io/package.py
+++ 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)