new package: polypolish (#33601)

* added polypolish package, comfirmed builds
* added bwa dep

1 files changed, 29 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/polypolish/package.py b/var/spack/repos/builtin/packages/polypolish/package.py
new file mode 100644
index 0000000000..1b1e99f282
--- /dev/null
+++ b/var/spack/repos/builtin/packages/polypolish/package.py
@@ -0,0 +1,29 @@
+# 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 Polypolish(Package):
+    """Polypolish is a tool for polishing genome assemblies with short reads.
+    Unlike other tools in this category, Polypolish uses SAM files where each
+    read has been aligned to all possible locations (not just a single best
+    location). This allows it to repair errors in repeat regions that other
+    alignment-based polishers cannot fix."""
+
+    homepage = "https://github.com/rrwick/Polypolish"
+    url = "https://github.com/rrwick/Polypolish/archive/refs/tags/v0.5.0.tar.gz"
+
+    version("0.5.0", sha256="183156093c03094290951f140010b3aef6222a672bf538e9136914178775fb1f")
+
+    depends_on("rust")
+    depends_on("python@3.6:", type="run")
+    depends_on("bwa", type="run")
+
+    def install(self, spec, prefix):
+        cargo = which("cargo")
+        cargo("install", "--root", prefix, "--path", ".")
+        install("scripts/polypolish_insert_filter.py", prefix.bin)