liftoff: add new package (#45726)

Signed-off-by: Shane Nehring <snehring@iastate.edu>

3 files changed, 73 insertions, 2 deletions

diff --git a/var/spack/repos/builtin/packages/liftoff/package.py b/var/spack/repos/builtin/packages/liftoff/package.py
new file mode 100644
index 0000000000..cbe9eb0f88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/liftoff/package.py
@@ -0,0 +1,39 @@
+# 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 Liftoff(PythonPackage):
+    """Liftoff is a tool that accurately maps annotations in GFF or
+    GTF between assemblies of the same, or closely-related species.
+    """
+
+    homepage = "https://github.com/agshumate/Liftoff"
+
+    pypi = "liftoff/Liftoff-1.6.3.2.tar.gz"
+
+    git = "https://github.com/agshumate/Liftoff.git"
+
+    maintainers("snehring")
+
+    license("GPL-3.0-only", checked_by="snehring")
+
+    version("1.6.3.2", sha256="7070a861144d0f043533893d39f95589a64d63f0365a99d06d71f1700b7fb758")
+
+    depends_on("python@3:", type=("build", "run"))
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-numpy@1.22:", type=("build", "run"))
+    depends_on("py-biopython@1.76:", type=("build", "run"))
+    depends_on("py-gffutils@0.10.1:", type=("build", "run"))
+    depends_on("py-networkx@2.4:", type=("build", "run"))
+    depends_on("py-pysam@0.19.1:", type=("build", "run"))
+    depends_on("py-pyfaidx@0.5.8:", type=("build", "run"))
+    depends_on("py-interlap@0.2.6:", type=("build", "run"))
+    depends_on("py-ujson@3:", type=("build", "run"))
+    depends_on("py-parasail@1.2.1:", type=("build", "run"))
+    depends_on("minimap2", type="run")
diff --git a/var/spack/repos/builtin/packages/py-interlap/package.py b/var/spack/repos/builtin/packages/py-interlap/package.py
new file mode 100644
index 0000000000..0990810990
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-interlap/package.py
@@ -0,0 +1,21 @@
+# 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 PyInterlap(PythonPackage):
+    """interlap: fast, simple interval overlap"""
+
+    homepage = "https://brentp.github.io/interlap/index.html"
+    pypi = "interlap/interlap-0.2.7.tar.gz"
+
+    maintainers("snehring")
+
+    license("MIT", checked_by="snehring")
+
+    version("0.2.7", sha256="31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9")
+
+    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-pyfaidx/package.py b/var/spack/repos/builtin/packages/py-pyfaidx/package.py
index 205f4e6a7f..3c3ebf2bf7 100644
--- a/var/spack/repos/builtin/packages/py-pyfaidx/package.py
+++ b/var/spack/repos/builtin/packages/py-pyfaidx/package.py
@@ -11,9 +11,20 @@ class PyPyfaidx(PythonPackage):
 
     pypi = "pyfaidx/pyfaidx-0.5.5.2.tar.gz"
 
+    maintainers("snehring")
+
     license("BSD-3-Clause")
 
+    version("0.8.1.2", sha256="d8452470455b1e778f93969447db8ea24deb4624c7c40769516459cb6f87bc33")
+    version("0.6.4", sha256="7ba3bdcb1df4ba749f7665b34e6a052aa4e842406a0df95e6df4717cc123f392")
     version("0.5.5.2", sha256="9ac22bdc7b9c5d995d32eb9dc278af9ba970481636ec75c0d687d38c26446caa")
 
-    depends_on("py-setuptools@0.7:", type=("build", "run"))
-    depends_on("py-six", type=("build", "run"))
+    depends_on("python@3.7:", type=("build", "run"), when="@0.8.1.2:")
+
+    depends_on("py-setuptools@0.7:", type="build")
+    depends_on("py-setuptools@45:", type="build", when="@0.8.1.2:")
+    depends_on("py-setuptools-scm", type="build", when="@0.8.1.2:")
+    depends_on("py-importlib-metadata", type="build", when="@0.8.1.2:")
+    depends_on("py-packaging", type=("build", "run"), when="@0.8.1.2:")
+
+    depends_on("py-six", type=("build", "run"), when="@:0.6.4")