Implement `odgi` package (#39078)

* feature (packages): implement `odgi` package
  This commit re-implements odgi package (superseded by #38741)
* fix (packages): remove redundant `requires()` from odgi package
  This commit removes redundant use of `requires()` for gcc version in the `odgi` package

1 files changed, 48 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/odgi/package.py b/var/spack/repos/builtin/packages/odgi/package.py
new file mode 100644
index 0000000000..459ab59bac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/odgi/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2023 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 Odgi(CMakePackage):
+    """Optimized dynamic genome/graph implementation.
+    Odgi provides an efficient and succinct dynamic DNA sequence graph model, as
+    well as a host of algorithms that allow the use of such graphs in
+    bioinformatic analyses.
+    """
+
+    homepage = "https://github.com/pangenome/odgi"
+    git = "https://github.com/pangenome/odgi.git"
+
+    # notify when the package is updated.
+    maintainers("tbhaxor", "EbiArnie")
+
+    # <<< Versions list starts here
+    version("0.8.3", commit="34f006f31c3f6b35a1eb8d58a4edb1c458583de3", submodules=True)
+    # >>> Versions list ends here
+
+    # compilation problem with ninja
+    generator("make", default="make")
+
+    # the range is required to successfully build the program
+    requires("%gcc", msg="Package odgi depends on the gcc C++ compiler")
+    conflicts(
+        "%gcc@:9.2,13:", msg="Unsupported compiler version. Recommended range is 9.3 -> 12.x"
+    )
+
+    # <<< Dependencies list starts here
+    depends_on("python")
+    depends_on("py-pybind11")
+    depends_on("sdsl-lite")
+    depends_on("libdivsufsort")
+    depends_on("jemalloc")
+    # >>> Dependencies list ends here
+
+    def cmake_args(self):
+        args = [
+            "-DCMAKE_CXX_STANDARD_REQUIRED:BOOL=ON",
+            "-DPYTHON_EXECUTABLE:FILEPATH={0}".format(self.spec["python"].command),
+        ]
+        return args