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| -rw-r--r-- | var/spack/repos/builtin/packages/isoquant/package.py | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/isoquant/package.py b/var/spack/repos/builtin/packages/isoquant/package.py new file mode 100644 index 0000000000..7655204ec5 --- /dev/null +++ b/var/spack/repos/builtin/packages/isoquant/package.py @@ -0,0 +1,45 @@ +# 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 Isoquant(Package): + """IsoQuant: Transcript discovery and quantification with long RNA reads""" + + # IsoQuant is a collection of Python scripts but does not install as a + # typical Python package, so this is a `Package` rather than a `PythonPackage` + # and we move things into place manually ... + + homepage = "https://ablab.github.io/IsoQuant/" + url = "https://github.com/ablab/IsoQuant/releases/download/v3.6.1/IsoQuant-3.6.1.tar.gz" + + license("GPL-2.0-only", checked_by="A-N-Other") + + version("3.6.1", sha256="6d16e47e9ca45f9a0d029940d5b84e03038d9ba3d640945e3a5087acfd7ed56d") + + depends_on("minimap2", type="run") + depends_on("samtools", type="run") + + depends_on("python@3.8:", type="run") + depends_on("py-gffutils@0.10.1:", type="run") + depends_on("py-biopython@1.76:", type="run") + depends_on("py-pandas@1.0.1:", type="run") + depends_on("py-pybedtools@0.8.1:", type="run") + depends_on("py-pysam@0.15:", type="run") + depends_on("py-packaging", type="run") + depends_on("py-pyfaidx@0.7:", type="run") + depends_on("py-pyyaml@5.4:", type="run") + depends_on("py-matplotlib@3.1.3:", type="run") + depends_on("py-numpy@1.18.1:", type="run") + depends_on("py-scipy@1.4.1:", type="run") + depends_on("py-seaborn@0.10.0:", type="run") + + def install(self, spec, prefix): + chmod = which("chmod") + chmod("+x", "isoquant.py", "visualize.py") + mkdirp(prefix.bin) + install("*.py", prefix.bin) + install_tree("src", prefix.bin.src) |