pharokka and py-phanotate: new packages (#34333)

* pharokka and py-phanotate: new packages

* move libxcrypt edit

I don't need libxcrypt when not building dev infernal. Moving to a different PR

2 files changed, 55 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/pharokka/package.py b/var/spack/repos/builtin/packages/pharokka/package.py
new file mode 100644
index 0000000000..11653ee96c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pharokka/package.py
@@ -0,0 +1,31 @@
+# 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 Pharokka(Package):
+    """pharokka is a rapid standardised annotation
+    pipeline for bacteriophage genomes"""
+
+    homepage = "https://github.com/gbouras13/pharokka"
+    url = "https://github.com/gbouras13/pharokka/archive/refs/tags/v1.1.0.tar.gz"
+
+    version("1.1.0", sha256="57d546f501f201117f5d8037ac47c0d83ccd1ec518080145e8f28d3e9843fba6")
+
+    depends_on("py-bcbio-gff", type="run")
+    depends_on("py-biopython@1.78:", type="run")
+    depends_on("py-phanotate@1.5.0:", type="run")
+    depends_on("py-pandas", type="run")
+    depends_on("mmseqs2@13.45111", type="run")
+    depends_on("trnascan-se@2.0.9:", type="run")
+    depends_on("prodigal@2.6.3:", type="run")
+    depends_on("minced@0.4.2:", type="run")
+    depends_on("aragorn@1.2.41:", type="run")
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree("bin", prefix.bin)
diff --git a/var/spack/repos/builtin/packages/py-phanotate/package.py b/var/spack/repos/builtin/packages/py-phanotate/package.py
new file mode 100644
index 0000000000..fdea8cb3b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-phanotate/package.py
@@ -0,0 +1,24 @@
+# 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 PyPhanotate(PythonPackage):
+    """PHANOTATE is a tool to annotate phage genomes. It uses the assumption
+    that non-coding bases in a phage genome is disadvantageous, and then
+    populates a weighted graph to find the optimal path through the six frames
+    of the DNA where open reading frames are beneficial paths, while gaps and
+    overlaps are penalized paths."""
+
+    homepage = "https://github.com/deprekate/phanotate"
+    pypi = "phanotate/phanotate-1.5.0.tar.gz"
+
+    version("1.5.0", sha256="589e441d2369e5550aef98b8d99fd079d130363bf881a70ac862fc7a8e0d2c88")
+
+    depends_on("python@3.5.3:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-fastpath@1.3:", type=("build", "run"))