perl-bio-bigfile: new package (#44505)

* Adding the perl-bio-db-bigfile package

* 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

* Removing unneeded dependencies

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

---------

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

1 files changed, 80 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/perl-bio-bigfile/package.py b/var/spack/repos/builtin/packages/perl-bio-bigfile/package.py
new file mode 100644
index 0000000000..b43d7ec1de
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-bio-bigfile/package.py
@@ -0,0 +1,80 @@
+# 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 PerlBioBigfile(PerlPackage):
+    """Bio::DB::BigFile -- Low-level interface to BigWig & BigBed files for perl"""
+
+    homepage = "https://metacpan.org/pod/Bio::DB::BigFile"
+    url = "https://cpan.metacpan.org/authors/id/L/LD/LDS/Bio-BigFile-1.07.tar.gz"
+
+    maintainers("teaguesterling")
+
+    license("Artistic-1.0-Perl OR GPL-1.0-or-later", checked_by="teaguesterling")
+
+    version("1.07", sha256="277b66ce8acbdd52399e2c5a0cf4e3bd5c74c12b94877cd383d0c4c97740d16d")
+    version("1.06", sha256="15f1ece2563096a301cff533a9ac91b8fc31af7643b4c4d7fd5d4fa75d4cb5ef")
+    version("1.05", sha256="1675662cfeff05a4e7289132481fd6cf8a15578bef0552b614047a03048fd057")
+    version("1.04", sha256="aef1db4cc4f4fb5b4d629719e16b50ec8d0b471d90e894060a88bd379647c4fa")
+    version("1.03", sha256="cb4c61c4d880661580f1964280a3731e31c952a3f7e973e7096b2377a6c62d29")
+    version("1.02", sha256="baab5010d2b1121c9f84fb1a8c873ced6e24882ef9bece1c3a2b455ed90925fd")
+    version("1.01", sha256="662310df5cad45f916c341e6b9a888323bd7b2d6a96957fdf8b0be73de7c3877")
+    version("1.00", sha256="925c9b94d5ea10db59911556fe87d4566e12032d13c70c574e74dc009cf73b91")
+
+    depends_on("perl-module-build", type="build")
+    depends_on("gmake", type="build")
+
+    with default_args(type=("build", "link")):
+        depends_on("kentutils")
+        depends_on("htslib+pic", when="^kentutils~builtin_htslib")
+        depends_on("openssl")
+
+    with default_args(type=("build", "run")):
+        depends_on("perl-bioperl")
+        depends_on("perl-io-string")
+
+    def build_pl_args(self):
+        # Need to tell the linker exactly where to find these
+        # dependencies as the perl build system hasn't been told
+        # they are needed. It explicitly searches for kentutils
+        # The includes will be recongized by CFLAGS but not the
+        # LIBS, which results in failures only once you try to
+        # to run the tests
+        incs = [
+            # This is usually set by Build.PL from KENT_SRC
+            f"-I{kentutils_include_dir}",
+            # Build system looks for tbx.h instead of htslib/tbx.h
+            # so we need to give it some special help for HTSLIB
+            f"-I{kentutils_htslib_include_dir.htslib}",
+        ]
+        libs = [
+            # This is usually set by Build.PL from KENT_SRC
+            join_path(kentutils_lib_dir, "jkweb.a"),
+            # These are being set in Build.PL so we need to reset here
+            "-lz",
+            "-lssl",
+            # This is an undocumented dependency from kentutils
+            "-lhts",
+        ]
+
+        return [
+            f"--extra_compiler_flags={' '.join(incs)}",
+            f"--extra_linker_flags={' '.join(libs)}",
+        ]
+
+    def setup_build_environment(self, env):
+        # These variables are exected by by the Build.PL file
+        # even though we override the results via PERL_MB_OPT
+        kent = self.spec["kentutils"]
+        env.set("KENT_SRC", kent.prefix)
+        env.set("MACHTYPE", kent.package.machtype)
+
+        # Overriding this explicitly as an environmental variable
+        # as the Build.PL script doesn't honnor the command line
+        # args and needs some extra coaxing to pass tests
+        # (The package builds fine without this but the tests fail)
+        args = [f"'{arg}'" for arg in self.build_pl_args()]
+        env.set("PERL_MB_OPT", " ".join(args))