zhangyiss/spack
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

hicup: new package @0.9.2 (#47008)

Browse Source 
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
This commit is contained in:
George Young 2024-10-19 01:53:23 +01:00 committed by GitHub
parent f69e8297a7
commit f2bd11cbf4
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
1 changed files with 55 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

55
var/spack/repos/builtin/packages/hicup/package.py Normal file
View File

@ -0,0 +1,55 @@
# 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)
from spack.package import *
class Hicup(Package):
"""HiCUP: a bioinformatics pipeline for processing Hi-C data"""
homepage = "https://stevenwingett.github.io/HiCUP"
url = "https://github.com/StevenWingett/HiCUP/archive/refs/tags/v0.9.2.tar.gz"
git = "https://github.com/StevenWingett/HiCUP.git"
license("LGPL-3.0-only", checked_by="A-N-Other")
version("0.9.2", sha256="7f9f65669d14fd2499afc4ac87735834b57b8f30b8e5785c4b406ec206cf9d2a")
version("0.8.3", sha256="e2381c2c45e0d79a6d1a2d9a8358b3efe8da727112d262cb0122132012266368")
version("combinations", branch="combinations")
variant("bowtie2", description="Use bowtie2 aligner", default=True)
variant("bowtie", description="Use bowtie aligner", default=False)
depends_on("pandoc", type="run")
depends_on("perl", type="run")
depends_on("perl-math-round", type="run")
depends_on("r", type="run")
depends_on("r-stringi@1.7.8:", type="run")
depends_on("r-markdown", type="run")
depends_on("r-tidyverse", type="run")
depends_on("r-plotly", type="run")
depends_on("samtools@0.1.18:", type="run")
# variant dependencies
depends_on("bowtie2", type="run", when="+bowtie2")
depends_on("bowtie", type="run", when="+bowtie")
def edit(self, spec, prefix):
grep = which("grep")
chmod = which("chmod")
perl_files = grep("-lRr", "#!/usr/bin/perl", ".").splitlines()
for f in perl_files:
filter_file("/usr/bin/perl", self.spec["perl"].command.path, f, backup=False)
filter_file("$Bin", "$RealBin", f, backup=False)
chmod("+x", f)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("hicup*", prefix.bin)
if self.spec.satisfies("@combinations"):
install("Misc/get_captured_reads", prefix.bin)
else:
install("Misc/hicup_capture", prefix.bin)
install("Conversion/hicup2*", prefix.bin)
install_tree("r_scripts", prefix.bin.r_scripts)