py-drep and ANIcalculator: new packages (#33467)

* py-drep: new package

* fixed file extension

* added darwin conflict

* py-checkm-genome and py-pysam: bumped version and updated deps (#10)

added checkm and pysam deps

* added dep documentation and fixed style

* changed checkm and pysam back to dev version for upstreaming

* added url and perl run dep

* fixed style

1 files changed, 44 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-drep/package.py b/var/spack/repos/builtin/packages/py-drep/package.py
new file mode 100644
index 0000000000..a7ec0b3d00
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-drep/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2022 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 PyDrep(PythonPackage):
+    """dRep is a python program for rapidly comparing large numbers of genomes.
+    dRep can also "de-replicate" a genome set by identifying groups of highly
+    similar genomes and choosing the best representative genome for each
+    genome set."""
+
+    homepage = "https://github.com/MrOlm/drep"
+    pypi = "drep/drep-3.4.0.tar.gz"
+
+    version("3.4.0", sha256="a6533eb585122c1ee66ae622b1b97450a3e1e493a3c3c1d55e79a580d5c46d40")
+
+    variant("fastani", default=True, description="Enable fastANI support")
+    variant("py-checkm-genome", default=True, description="Enable CheckM support")
+    variant("anicalculator", default=True, description="Enable gDNA support")
+    variant("prodigal", default=True, description="Used with both checkM and gANI")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-seaborn", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-biopython", type=("build", "run"))
+    depends_on("py-scikit-learn", type=("build", "run"))
+    depends_on("py-tqdm", type=("build", "run"))
+    depends_on("py-pytest", type=("build", "run"))
+    # Non-python dependencies
+    # https://drep.readthedocs.io/en/latest/installation.html#dependencies
+    # essential dependencies
+    depends_on("mash@1.1.1:", type="run")
+    depends_on("mummer@3.23:", type="run")
+    # recommended dependencies
+    depends_on("fastani", type="run", when="+fastani")
+    depends_on("py-checkm-genome@1.0.7:", type="run", when="+py-checkm-genome")
+    depends_on("anicalculator@1:", type="run", when="+anicalculator")
+    depends_on("prodigal@2.6.3:", type="run", when="+prodigal")