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| author | Luke Diorio-Toth <ldioriototh@gmail.com> | 2022-10-31 17:07:40 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-10-31 15:07:40 -0700 |
| commit | 02097b18560934698fee5279807e59ca43fa4182 (patch) | |
| tree | 7b56f8f3b8e14c8e317f36a0eae969bcbc482282 /var | |
| parent | a83456dd7b4aef6044df5f3449dcbedc83b7784a (diff) | |
| download | spack-02097b18560934698fee5279807e59ca43fa4182.tar.gz spack-02097b18560934698fee5279807e59ca43fa4182.tar.bz2 spack-02097b18560934698fee5279807e59ca43fa4182.tar.xz spack-02097b18560934698fee5279807e59ca43fa4182.zip | |
new package: polypolish (#33601)
* added polypolish package, comfirmed builds
* added bwa dep
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/polypolish/package.py | 29 |
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) |