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authorLuke Diorio-Toth <ldioriototh@gmail.com>2022-10-31 17:07:40 -0500
committerGitHub <noreply@github.com>2022-10-31 15:07:40 -0700
commit02097b18560934698fee5279807e59ca43fa4182 (patch)
tree7b56f8f3b8e14c8e317f36a0eae969bcbc482282
parenta83456dd7b4aef6044df5f3449dcbedc83b7784a (diff)
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new package: polypolish (#33601)
* added polypolish package, comfirmed builds * added bwa dep
-rw-r--r--var/spack/repos/builtin/packages/polypolish/package.py29
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)