This repository has been archived by the owner on Aug 6, 2024. It is now read-only.
forked from MultiQC/MultiQC
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsetup.py
executable file
·251 lines (236 loc) · 12.4 KB
/
setup.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
#!/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 = "1.15dev"
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="[email protected]",
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",
"pyyaml>=4",
"requests",
"rich>=10",
"rich-click",
"simplejson",
"spectra>=0.0.10",
],
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",
"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",
"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",
"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",
"lima = multiqc.modules.lima:MultiqcModule",
"longranger = multiqc.modules.longranger:MultiqcModule",
"macs2 = multiqc.modules.macs2:MultiqcModule",
"malt = multiqc.modules.malt: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",
"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
"""
)