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# Copyright 2013-2022 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 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"
maintainers = ['glennpj']
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', when='^python@3:')
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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