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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 Seqera Labs (https://seqera.io/), originally at SciLifeLab Sweden (http://www.scilifelab.se)
"""
from setuptools import find_packages, setup
version = "1.17dev"
dl_version = "master" if "dev" in version else "v{}".format(version)
print(
f"""-----------------------------------
Installing MultiQC version {version}
-----------------------------------
"""
)
setup(
name="multiqc",
version=version,
author="Phil Ewels",
author_email="phil.ewels@seqera.io",
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,
install_requires=[
"matplotlib>=2.1.1",
"networkx>=2.5.1",
"numpy",
"click",
"coloredlogs",
"future>0.14.0",
"jinja2>=3.0.0",
"lzstring",
"markdown",
"packaging",
"pyyaml>=4",
"requests",
"rich>=10",
"rich-click",
"spectra>=0.0.10",
"importlib-metadata",
],
entry_points={
"console_scripts": [
"multiqc=multiqc.__main__:run_multiqc",
],
"multiqc.modules.v1": [
"adapterRemoval = multiqc.modules.adapterRemoval:MultiqcModule",
"afterqc = multiqc.modules.afterqc:MultiqcModule",
"anglerfish = multiqc.modules.anglerfish:MultiqcModule",
"bakta = multiqc.modules.bakta:MultiqcModule",
"bamtools = multiqc.modules.bamtools:MultiqcModule",
"bbduk = multiqc.modules.bbduk:MultiqcModule",
"bbmap = multiqc.modules.bbmap:MultiqcModule",
"bcftools = multiqc.modules.bcftools:MultiqcModule",
"bcl2fastq = multiqc.modules.bcl2fastq:MultiqcModule",
"bclconvert = multiqc.modules.bclconvert:MultiqcModule",
"biobambam2 = multiqc.modules.biobambam2:MultiqcModule",
"biobloomtools = multiqc.modules.biobloomtools:MultiqcModule",
"biscuit = multiqc.modules.biscuit:MultiqcModule",
"bismark = multiqc.modules.bismark:MultiqcModule",
"bowtie1 = multiqc.modules.bowtie1:MultiqcModule",
"bowtie2 = multiqc.modules.bowtie2:MultiqcModule",
"bracken = multiqc.modules.bracken:MultiqcModule",
"busco = multiqc.modules.busco:MultiqcModule",
"bustools = multiqc.modules.bustools:MultiqcModule",
"ccs = multiqc.modules.ccs:MultiqcModule",
"cellranger = multiqc.modules.cellranger:MultiqcModule",
"checkqc = multiqc.modules.checkqc: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",
"dedup = multiqc.modules.dedup:MultiqcModule",
"deeptools = multiqc.modules.deeptools:MultiqcModule",
"diamond = multiqc.modules.diamond:MultiqcModule",
"disambiguate = multiqc.modules.disambiguate:MultiqcModule",
"dragen = multiqc.modules.dragen:MultiqcModule",
"dragen_fastqc = multiqc.modules.dragen_fastqc:MultiqcModule",
"eigenstratdatabasetools = multiqc.modules.eigenstratdatabasetools:MultiqcModule",
"fastp = multiqc.modules.fastp:MultiqcModule",
"fastq_screen = multiqc.modules.fastq_screen:MultiqcModule",
"fastqc = multiqc.modules.fastqc:MultiqcModule",
"featureCounts = multiqc.modules.featureCounts:MultiqcModule",
"fgbio = multiqc.modules.fgbio:MultiqcModule",
"flash = multiqc.modules.flash:MultiqcModule",
"flexbar = multiqc.modules.flexbar:MultiqcModule",
"filtlong = multiqc.modules.filtlong:MultiqcModule",
"freyja = multiqc.modules.freyja:MultiqcModule",
"gffcompare = multiqc.modules.gffcompare:MultiqcModule",
"gatk = multiqc.modules.gatk:MultiqcModule",
"goleft_indexcov = multiqc.modules.goleft_indexcov:MultiqcModule",
"gopeaks = multiqc.modules.gopeaks:MultiqcModule",
"happy = multiqc.modules.happy:MultiqcModule",
"hicexplorer = multiqc.modules.hicexplorer:MultiqcModule",
"hicpro = multiqc.modules.hicpro:MultiqcModule",
"hicup = multiqc.modules.hicup:MultiqcModule",
"hifiasm = multiqc.modules.hifiasm:MultiqcModule",
"hisat2 = multiqc.modules.hisat2:MultiqcModule",
"homer = multiqc.modules.homer:MultiqcModule",
"hops = multiqc.modules.hops:MultiqcModule",
"htseq = multiqc.modules.htseq:MultiqcModule",
"humid = multiqc.modules.humid:MultiqcModule",
"interop = multiqc.modules.interop:MultiqcModule",
"ivar = multiqc.modules.ivar:MultiqcModule",
"jcvi = multiqc.modules.jcvi:MultiqcModule",
"jellyfish = multiqc.modules.jellyfish:MultiqcModule",
"kaiju = multiqc.modules.kaiju:MultiqcModule",
"kallisto = multiqc.modules.kallisto:MultiqcModule",
"kat = multiqc.modules.kat:MultiqcModule",
"kraken = multiqc.modules.kraken:MultiqcModule",
"leehom = multiqc.modules.leehom:MultiqcModule",
"librarian = multiqc.modules.librarian:MultiqcModule",
"lima = multiqc.modules.lima:MultiqcModule",
"longranger = multiqc.modules.longranger:MultiqcModule",
"macs2 = multiqc.modules.macs2:MultiqcModule",
"malt = multiqc.modules.malt:MultiqcModule",
"mapdamage = multiqc.modules.mapdamage:MultiqcModule",
"methylQA = multiqc.modules.methylQA:MultiqcModule",
"minionqc = multiqc.modules.minionqc:MultiqcModule",
"mirtop = multiqc.modules.mirtop:MultiqcModule",
"mirtrace = multiqc.modules.mirtrace:MultiqcModule",
"mosdepth = multiqc.modules.mosdepth:MultiqcModule",
"motus = multiqc.modules.motus:MultiqcModule",
"mtnucratio = multiqc.modules.mtnucratio:MultiqcModule",
"multivcfanalyzer = multiqc.modules.multivcfanalyzer:MultiqcModule",
"nanostat = multiqc.modules.nanostat:MultiqcModule",
"nextclade = multiqc.modules.nextclade:MultiqcModule",
"ngsderive = multiqc.modules.ngsderive:MultiqcModule",
"odgi = multiqc.modules.odgi:MultiqcModule",
"optitype = multiqc.modules.optitype:MultiqcModule",
"pangolin = multiqc.modules.pangolin:MultiqcModule",
"pbmarkdup = multiqc.modules.pbmarkdup:MultiqcModule",
"peddy = multiqc.modules.peddy:MultiqcModule",
"phantompeakqualtools = multiqc.modules.phantompeakqualtools:MultiqcModule",
"picard = multiqc.modules.picard:MultiqcModule",
"porechop = multiqc.modules.porechop:MultiqcModule",
"preseq = multiqc.modules.preseq:MultiqcModule",
"prinseqplusplus = multiqc.modules.prinseqplusplus:MultiqcModule",
"prokka = multiqc.modules.prokka:MultiqcModule",
"purple = multiqc.modules.purple:MultiqcModule",
"pychopper = multiqc.modules.pychopper:MultiqcModule",
"pycoqc = multiqc.modules.pycoqc:MultiqcModule",
"qc3C = multiqc.modules.qc3C:MultiqcModule",
"qorts = multiqc.modules.qorts:MultiqcModule",
"qualimap = multiqc.modules.qualimap:MultiqcModule",
"quast = multiqc.modules.quast:MultiqcModule",
"rna_seqc = multiqc.modules.rna_seqc:MultiqcModule",
"rockhopper = multiqc.modules.rockhopper:MultiqcModule",
"rsem = multiqc.modules.rsem:MultiqcModule",
"rseqc = multiqc.modules.rseqc:MultiqcModule",
"salmon = multiqc.modules.salmon:MultiqcModule",
"sambamba = multiqc.modules.sambamba:MultiqcModule",
"samblaster = multiqc.modules.samblaster:MultiqcModule",
"samtools = multiqc.modules.samtools:MultiqcModule",
"sargasso = multiqc.modules.sargasso:MultiqcModule",
"sentieon = multiqc.modules.sentieon:MultiqcModule",
"seqyclean = multiqc.modules.seqyclean:MultiqcModule",
"sexdeterrmine = multiqc.modules.sexdeterrmine:MultiqcModule",
"sickle = multiqc.modules.sickle:MultiqcModule",
"skewer = multiqc.modules.skewer:MultiqcModule",
"slamdunk = multiqc.modules.slamdunk:MultiqcModule",
"snippy = multiqc.modules.snippy:MultiqcModule",
"snpeff = multiqc.modules.snpeff:MultiqcModule",
"snpsplit = multiqc.modules.snpsplit:MultiqcModule",
"somalier = multiqc.modules.somalier:MultiqcModule",
"sortmerna = multiqc.modules.sortmerna:MultiqcModule",
"sourmash = multiqc.modules.sourmash: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",
"umitools = multiqc.modules.umitools:MultiqcModule",
"varscan2 = multiqc.modules.varscan2:MultiqcModule",
"vcftools = multiqc.modules.vcftools:MultiqcModule",
"vep = multiqc.modules.vep:MultiqcModule",
"verifybamid = multiqc.modules.verifybamid:MultiqcModule",
"whatshap = multiqc.modules.whatshap:MultiqcModule",
],
"multiqc.templates.v1": [
"default = multiqc.templates.default",
"default_dev = multiqc.templates.default_dev",
"sections = multiqc.templates.sections",
"simple = multiqc.templates.simple",
"gathered = multiqc.templates.gathered",
"geo = multiqc.templates.geo",
],
## See https://multiqc.info/docs/#multiqc-plugins for documentation
# '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 :: 5 - Production/Stable",
"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
"""
)