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-rw-r--r--var/spack/repos/builtin/packages/anicalculator/package.py35
-rw-r--r--var/spack/repos/builtin/packages/py-drep/package.py44
2 files changed, 79 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/anicalculator/package.py b/var/spack/repos/builtin/packages/anicalculator/package.py
new file mode 100644
index 0000000000..7d83bb4596
--- /dev/null
+++ b/var/spack/repos/builtin/packages/anicalculator/package.py
@@ -0,0 +1,35 @@
+# 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)
+
+import os
+
+from spack.package import *
+
+
+class Anicalculator(Package):
+ """This tool will calculate the bidirectional average nucleotide identity
+ (gANI) and Alignment Fraction (AF) between two genomes.
+
+ Note: A manual download is required for ANIcalculator.
+ Spack will search your current directory for the download file.
+ Alternatively, add this file to a mirror so that Spack can find it.
+ For instructions on how to set up a mirror, see
+ https://spack.readthedocs.io/en/latest/mirrors.html"""
+
+ homepage = "https://ani.jgi.doe.gov/html/download.php?"
+ url = "file://{0}/ANIcalculator_v1.tgz".format(os.getcwd())
+ manual_download = True
+
+ version("1", sha256="236596a9a204cbcad162fc66be3506b2530b1f48f4f84d9647ccec3ca7483a43")
+
+ depends_on("perl@5:", type="run")
+
+ conflicts("platform=darwin", msg="ANIcalculator requires Linux")
+
+ def install(self, spec, prefix):
+ mkdirp(prefix.bin)
+ install("ANIcalculator", prefix.bin)
+ install("nsimscan", prefix.bin)
+ install_tree("Log", prefix.bin.Log)
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")