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| author | George Young <A-N-Other@users.noreply.github.com> | 2024-10-19 01:53:23 +0100 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2024-10-18 18:53:23 -0600 |
| commit | f2bd11cbf439a7ee3ff8c16a838c325915472553 (patch) | |
| tree | 7b7b3a67be15a066ff37ae1ab045a60417527147 /var | |
| parent | f69e8297a760dbb615f5b6b2c55505d4bf12fdde (diff) | |
| download | spack-f2bd11cbf439a7ee3ff8c16a838c325915472553.tar.gz spack-f2bd11cbf439a7ee3ff8c16a838c325915472553.tar.bz2 spack-f2bd11cbf439a7ee3ff8c16a838c325915472553.tar.xz spack-f2bd11cbf439a7ee3ff8c16a838c325915472553.zip | |
hicup: new package @0.9.2 (#47008)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/hicup/package.py | 55 |
1 files changed, 55 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/hicup/package.py b/var/spack/repos/builtin/packages/hicup/package.py new file mode 100644 index 0000000000..daf3f5da39 --- /dev/null +++ b/var/spack/repos/builtin/packages/hicup/package.py @@ -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) |