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seacr: new package @1.4-b2 (#42677)

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* seacr: new package @1.4-b2

* Update var/spack/repos/builtin/packages/seacr/package.py

Co-authored-by: Alec Scott <hi@alecbcs.com>

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <hi@alecbcs.com>
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George Young 2024-06-18 15:37:58 +01:00 committed by GitHub
parent 3b35b7f4fa
commit d911b9c48d
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var/spack/repos/builtin/packages/seacr/package.py Normal file
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# Copyright 2013-2024 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 Seacr(Package):
"""SEACR (Sparse Enrichment Analysis for CUT&RUN) is intended to call peaks and
enriched regions from sparse CUT&RUN or chromatin profiling data in which the
background is dominated by zeros"""
homepage = "https://github.com/FredHutch/SEACR"
git = "https://github.com/FredHutch/SEACR.git"
license("GPL-2.0-only", checked_by="A-N-Other")
version("1.4-b2", tag="v1.4-beta.2", commit="5179a70494eb129fcb1d640177de73f6509654e7")
version("1.3", tag="v1.3", commit="5a0efe59f06fb17cf9d34d415bb0c1a1f7a77a3c", preferred=True)
# Dependencies as per the README.md
depends_on("r", type="run")
depends_on("bedtools2", type="run")
def install(self, spec, prefix):
mkdirp(prefix.bin)
script_name = f"SEACR_{self.version.up_to(2)}"
os.chmod(f"{script_name}.sh", 0o755)
install(f"{script_name}.sh", prefix.bin.SEACR)
install(f"{script_name}.R", prefix.bin)