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# Copyright 2013-2023 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 Reditools(PythonPackage):
"""REDItools: python scripts for RNA editing detection by RNA-Seq data.
REDItools are simple python scripts conceived to facilitate the
investigation of RNA editing at large-scale and devoted to research groups
that would to explore such phenomenon in own data but don't have sufficient
bioinformatics skills. They work on main operating systems (although
unix/linux-based OS are preferred), can handle reads from whatever platform
in the standard BAM format and implement a variety of filters."""
homepage = "https://github.com/BioinfoUNIBA/REDItools"
git = "https://github.com/BioinfoUNIBA/REDItools.git"
license("MIT")
version("1.3_2020-08-03", commit="2dc71277a25e667797c363d1fca22726249774a3")
version("1.3_2020-03-20", commit="cf47f3d54f324aeb9650bcf8bfacf5a967762a55")
variant(
"nature_protocol",
default=False,
description="Install the Nature Protocol scripts and files",
)
# pip silently replaces distutils with setuptools
depends_on("py-setuptools", type="build")
depends_on("py-reindent", type="build")
depends_on("blat", type="run")
depends_on("py-fisher", type="run")
depends_on("py-numpy", type="run")
depends_on("py-pandas", type="run")
depends_on("py-pysam", type="run")
depends_on("py-scipy", type="run")
depends_on("tabix", type="run")
# Nature Protocol
depends_on("bcftools", type="run", when="+nature_protocol")
depends_on("bedtools2", type="run", when="+nature_protocol")
depends_on("bwa", type="run", when="+nature_protocol")
depends_on("bzip2", type="run", when="+nature_protocol")
depends_on("fastp", type="run", when="+nature_protocol")
depends_on("fastqc", type="run", when="+nature_protocol")
depends_on("git", type="run", when="+nature_protocol")
depends_on("gmap-gsnap", type="run", when="+nature_protocol")
depends_on("htslib", type="run", when="+nature_protocol")
depends_on("libdeflate", type="run", when="+nature_protocol")
depends_on("py-bx-python", type="run", when="+nature_protocol")
depends_on("py-rseqc", type="run", when="+nature_protocol")
depends_on("samtools", type="run", when="+nature_protocol")
depends_on("star", type="run", when="+nature_protocol")
depends_on("wget", type="run", when="+nature_protocol")
patch("interpreter.patch")
patch("setup.py.patch")
patch("batch_sort.patch", when="^python@3:")
@run_before("install")
def p2_to_p3(self):
if "^python@3:" in self.spec:
# clean up space/tab mixing
reindent = which("reindent")
reindent("--nobackup", "--recurse", ".")
# convert to be python3 compatible
p2_to_p3 = which("2to3")
p2_to_p3("--nobackups", "--write", ".")
@run_after("install")
def nature_protocol(self):
if "+nature_protocol" in self.spec:
mkdirp(prefix.NPfiles)
install_tree("NPfiles", prefix.NPfiles)
ignore_files = [
"conda_pckg_installer_docker.py",
"conda_pckgs_installer.py",
"download-prepare-data-NP_docker.py",
]
docker_conda = lambda p: p in ignore_files
install_tree("NPscripts", prefix.bin, ignore=docker_conda)
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