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setup.py
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setup.py
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#!/usr/bin/env python
"""
MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It is written in Python and contains modules for a large number of common bioinformatics tools.
You can install MultiQC from PyPI as follows::
pip install multiqc
Then it's just a case of going to your analysis directory and running the script::
multiqc .
MultiQC will scan the specified directory (:code:`'.'` is the current dir) and produce a report detailing whatever it finds.
The report is created in :code:`multiqc_report.html` by default. Tab-delimited data files are created in :code:`multiqc_data/` to give easy access for downstream processing.
For more detailed instructions, run :code:`multiqc -h`
See the MultiQC website for documentation and tutorial videos: http://multiqc.info
MultiQC was written by Phil Ewels (http://phil.ewels.co.uk) at SciLifeLab Sweden (http://www.scilifelab.se)
"""
from setuptools import setup, find_packages
import sys
version = '1.8dev'
dl_version = 'master' if 'dev' in version else 'v{}'.format(version)
print("""-----------------------------------
Installing MultiQC version {}
-----------------------------------
""".format(version))
install_requires = [
'click',
'future>0.14.0',
'lzstring',
'jinja2>=2.9',
'matplotlib>=2.1.1,<3.0.0',
'markdown',
'numpy',
'pyyaml>=4',
'requests',
'simplejson',
'spectra>=0.0.10'
]
setup(
name = 'multiqc',
version = version,
author = 'Phil Ewels',
author_email = 'phil.ewels@scilifelab.se',
description = "Create aggregate bioinformatics analysis reports across many samples and tools",
long_description = __doc__,
keywords = ['bioinformatics', 'biology', 'sequencing', 'NGS', 'next generation sequencing', 'quality control'],
url = 'http://multiqc.info',
download_url = 'https://github.com/ewels/MultiQC/tarball/{}'.format(dl_version),
license = 'GPLv3',
packages = find_packages(),
include_package_data = True,
zip_safe = False,
scripts = ['scripts/multiqc'],
install_requires = install_requires,
entry_points = {
'multiqc.modules.v1': [
'adapterRemoval = multiqc.modules.adapterRemoval:MultiqcModule',
'afterqc = multiqc.modules.afterqc:MultiqcModule',
'bamtools = multiqc.modules.bamtools:MultiqcModule',
'bbmap = multiqc.modules.bbmap:MultiqcModule',
'bcftools = multiqc.modules.bcftools:MultiqcModule',
'bcl2fastq = multiqc.modules.bcl2fastq:MultiqcModule',
'biobambam2 = multiqc.modules.biobambam2:MultiqcModule',
'biobloomtools = multiqc.modules.biobloomtools:MultiqcModule',
'bismark = multiqc.modules.bismark:MultiqcModule',
'biscuit = multiqc.modules.biscuit:MultiqcModule',
'bowtie1 = multiqc.modules.bowtie1:MultiqcModule',
'bowtie2 = multiqc.modules.bowtie2:MultiqcModule',
'busco = multiqc.modules.busco:MultiqcModule',
'clipandmerge = multiqc.modules.clipandmerge:MultiqcModule',
'clusterflow = multiqc.modules.clusterflow:MultiqcModule',
'conpair = multiqc.modules.conpair:MultiqcModule',
'custom_content = multiqc.modules.custom_content:custom_module_classes', # special case
'cutadapt = multiqc.modules.cutadapt:MultiqcModule',
'damageprofiler = multiqc.modules.damageprofiler:MultiqcModule',
'disambiguate = multiqc.modules.disambiguate:MultiqcModule',
'dedup = multiqc.modules.dedup:MultiqcModule',
'deeptools = multiqc.modules.deeptools:MultiqcModule',
'fastp = multiqc.modules.fastp:MultiqcModule',
'fastq_screen = multiqc.modules.fastq_screen:MultiqcModule',
'fastqc = multiqc.modules.fastqc:MultiqcModule',
'featureCounts = multiqc.modules.featureCounts:MultiqcModule',
'flash = multiqc.modules.flash:MultiqcModule',
'flexbar = multiqc.modules.flexbar:MultiqcModule',
'gatk = multiqc.modules.gatk:MultiqcModule',
'goleft_indexcov = multiqc.modules.goleft_indexcov:MultiqcModule',
'happy = multiqc.modules.happy:MultiqcModule',
'hicexplorer = multiqc.modules.hicexplorer:MultiqcModule',
'hicup = multiqc.modules.hicup:MultiqcModule',
'hicpro = multiqc.modules.hicpro:MultiqcModule',
'hisat2 = multiqc.modules.hisat2:MultiqcModule',
'homer = multiqc.modules.homer:MultiqcModule',
'htseq = multiqc.modules.htseq:MultiqcModule',
'interop = multiqc.modules.interop:MultiqcModule',
'jellyfish = multiqc.modules.jellyfish:MultiqcModule',
'kallisto = multiqc.modules.kallisto:MultiqcModule',
'kat = multiqc.modules.kat:MultiqcModule',
'leehom = multiqc.modules.leehom:MultiqcModule',
'longranger = multiqc.modules.longranger:MultiqcModule',
'macs2 = multiqc.modules.macs2:MultiqcModule',
'methylQA = multiqc.modules.methylQA:MultiqcModule',
'mirtrace = multiqc.modules.mirtrace:MultiqcModule',
'minionqc = multiqc.modules.minionqc:MultiqcModule',
'peddy = multiqc.modules.peddy:MultiqcModule',
'phantompeakqualtools = multiqc.modules.phantompeakqualtools:MultiqcModule',
'picard = multiqc.modules.picard:MultiqcModule',
'preseq = multiqc.modules.preseq:MultiqcModule',
'prokka = multiqc.modules.prokka:MultiqcModule',
'qorts = multiqc.modules.qorts:MultiqcModule',
'qualimap = multiqc.modules.qualimap:MultiqcModule',
'quast = multiqc.modules.quast:MultiqcModule',
'rna_seqc = multiqc.modules.rna_seqc:MultiqcModule',
'rsem = multiqc.modules.rsem:MultiqcModule',
'rseqc = multiqc.modules.rseqc:MultiqcModule',
'salmon = multiqc.modules.salmon:MultiqcModule',
'samblaster = multiqc.modules.samblaster:MultiqcModule',
'samtools = multiqc.modules.samtools:MultiqcModule',
'sargasso = multiqc.modules.sargasso:MultiqcModule',
'skewer = multiqc.modules.skewer:MultiqcModule',
'slamdunk = multiqc.modules.slamdunk:MultiqcModule',
'snpeff = multiqc.modules.snpeff:MultiqcModule',
'sortmerna = multiqc.modules.sortmerna:MultiqcModule',
'stacks = multiqc.modules.stacks:MultiqcModule',
'star = multiqc.modules.star:MultiqcModule',
'supernova = multiqc.modules.supernova:MultiqcModule',
'theta2 = multiqc.modules.theta2:MultiqcModule',
'tophat = multiqc.modules.tophat:MultiqcModule',
'trimmomatic = multiqc.modules.trimmomatic:MultiqcModule',
'vcftools = multiqc.modules.vcftools:MultiqcModule',
'verifybamid = multiqc.modules.verifybamid:MultiqcModule'
],
'multiqc.templates.v1': [
'default = multiqc.templates.default',
'default_dev = multiqc.templates.default_dev',
'sections = multiqc.templates.sections',
'simple = multiqc.templates.simple',
'geo = multiqc.templates.geo',
],
# 'multiqc.cli_options.v1': [
# 'my-new-option = myplugin.cli:new_option'
# ],
# 'multiqc.hooks.v1': [
# 'before_config = myplugin.hooks:before_config',
# 'config_loaded = myplugin.hooks:config_loaded',
# 'execution_start = myplugin.hooks:execution_start',
# 'before_modules = myplugin.hooks:before_modules',
# 'after_modules = myplugin.hooks:after_modules',
# 'before_report_generation = myplugin.hooks:before_report_generation',
# 'execution_finish = myplugin.hooks:execution_finish',
# ]
},
classifiers = [
'Development Status :: 4 - Beta',
'Environment :: Console',
'Environment :: Web Environment',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'Natural Language :: English',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX',
'Operating System :: Unix',
'Programming Language :: Python',
'Programming Language :: JavaScript',
'Topic :: Scientific/Engineering',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Visualization',
],
)
print("""
--------------------------------
MultiQC installation complete!
--------------------------------
For help in running MultiQC, please see the documentation available
at http://multiqc.info or run: multiqc --help
""")