--- a
+++ b/setup.py
@@ -0,0 +1,176 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+from setuptools import setup
+import os
+import sys
+
+_here = os.path.abspath(os.path.dirname(__file__))
+version = {}
+with open(os.path.join(_here, 'singlecellmultiomics', 'version.py')) as f:
+    exec(f.read(), version)
+
+if sys.version_info[0] < 3:
+    with open(os.path.join(_here, 'README.md')) as f:
+        long_description = f.read()
+else:
+    with open(os.path.join(_here, 'README.md'), encoding='utf-8') as f:
+        long_description = f.read()
+
+setup(
+
+    name='singlecellmultiomics',
+    version=version['__version__'],
+    description='Tools to deal with one or more measurements from single cells',
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    author='Buys de Barbanson',
+    author_email='b.barbanson@hubrecht.eu',
+    url='https://github.com/BuysDB/SingleCellMultiOmics',
+    download_url = 'https://github.com/BuysDB/SingleCellMultiOmics/archive/v0.1.9.tar.gz',
+
+    license='MIT',
+    packages=['singlecellmultiomics',
+
+        'singlecellmultiomics.alleleTools',
+        'singlecellmultiomics.bamProcessing',
+        'singlecellmultiomics.barcodeFileParser',
+        'singlecellmultiomics.countTableProcessing',
+        'singlecellmultiomics.features',
+        'singlecellmultiomics.fragment',
+        'singlecellmultiomics.fastqProcessing',
+        'singlecellmultiomics.fastaProcessing',
+        'singlecellmultiomics.libraryDetection',
+        'singlecellmultiomics.libraryProcessing',
+        'singlecellmultiomics.modularDemultiplexer',
+        'singlecellmultiomics.molecule',
+        'singlecellmultiomics.methylation',
+        'singlecellmultiomics.pyutils',
+        'singlecellmultiomics.variants',
+        'singlecellmultiomics.tags',
+        'singlecellmultiomics.statistic',
+        'singlecellmultiomics.tagtools',
+        'singlecellmultiomics.universalBamTagger',
+        'singlecellmultiomics.utils',
+        'singlecellmultiomics.modularDemultiplexer.demultiplexModules'
+        ],
+
+
+    scripts=[
+        # Demultiplexing
+        'singlecellmultiomics/modularDemultiplexer/demux.py',
+
+        # Fasta
+        'singlecellmultiomics/fastaProcessing/fastaMaskVariants.py',
+        'singlecellmultiomics/fastaProcessing/createMappabilityIndex.py',
+        'singlecellmultiomics/fastaProcessing/fastaCreateDict.py',
+
+        # Fastq
+        'singlecellmultiomics/fastqProcessing/fastq_filter_by_dt.py',
+
+        # Tagging
+        'singlecellmultiomics/universalBamTagger/universalBamTagger.py',
+        'singlecellmultiomics/universalBamTagger/bamtagmultiome_multi.py',
+        'singlecellmultiomics/universalBamTagger/bamtagmultiome.py',
+        'singlecellmultiomics/universalBamTagger/tapsTagger.py',
+        'singlecellmultiomics/universalBamTagger/tapsTabulator.py',
+        'singlecellmultiomics/universalBamTagger/4SUtagger.py',
+
+        # Methylation:
+        'singlecellmultiomics/methylation/methylationtab_to_bed.py',
+        'singlecellmultiomics/methylation/bam_to_methylation_bw.py',
+
+        # Bam processing:
+        'singlecellmultiomics/bamProcessing/bamTabulator.py',
+        'singlecellmultiomics/bamProcessing/bamCountRegions.py',
+        'singlecellmultiomics/bamProcessing/bamToNucleosomePositions.py',
+        'singlecellmultiomics/bamProcessing/bamAnalyzeCutDistances.py',
+        'singlecellmultiomics/bamProcessing/bamSplitByTag.py',
+        'singlecellmultiomics/bamProcessing/bamReadGroupFormat.py',
+        'singlecellmultiomics/bamProcessing/bamSetReadGroup.py',
+        'singlecellmultiomics/bamProcessing/bamToCountTable.py',
+        'singlecellmultiomics/bamProcessing/bamCopyNumber.py',
+        'singlecellmultiomics/bamProcessing/bamExtractSamples.py',
+        'singlecellmultiomics/bamProcessing/scmoConvert.py',
+        'singlecellmultiomics/bamProcessing/bamToMethylationAndCopyNumber.py',
+        'singlecellmultiomics/bamProcessing/bamDinucleotideDistribution.py',
+        'singlecellmultiomics/bamProcessing/bamToMethylationCalls.py',
+        'singlecellmultiomics/bamProcessing/bamMappingRate.py',
+        'singlecellmultiomics/bamProcessing/bamFilter.py',
+        'singlecellmultiomics/bamProcessing/bamPlotRTstats.py',
+        'singlecellmultiomics/bamProcessing/bamPlateVisualisation.py',
+        'singlecellmultiomics/bamProcessing/bamFeatureDensityVisualisation.py',
+        'singlecellmultiomics/bamProcessing/bamMethylationCutDistance.py',
+        'singlecellmultiomics/bamProcessing/bamDuprate.py',
+        'singlecellmultiomics/bamProcessing/bamExtractRandomPrimerStats.py',
+        'singlecellmultiomics/bamProcessing/bamToRNACounts.py',
+        'singlecellmultiomics/bamProcessing/bamToBigWig.py',
+        'singlecellmultiomics/bamProcessing/structureTensor.py',
+        'singlecellmultiomics/bamProcessing/bamCompare.py',
+        'singlecellmultiomics/bamProcessing/variantStats.py',
+        'singlecellmultiomics/bamProcessing/bamExtractVariants.py',
+        'singlecellmultiomics/bamProcessing/bamMatchGATKBQSRReport.py',
+        'singlecellmultiomics/bamProcessing/bamBinCounts.py',
+        'singlecellmultiomics/bamProcessing/bamExtractNearMolecules.py',
+        'singlecellmultiomics/bamProcessing/split_double_BAM.py',
+        'singlecellmultiomics/bamProcessing/bamOverseq.py',
+        'singlecellmultiomics/bamProcessing/plotRegion.py',
+        'singlecellmultiomics/bamProcessing/soft_clip_filter.py',
+        'singlecellmultiomics/utils/base_call_covariates.py',
+        'singlecellmultiomics/bamProcessing/estimateTapsConversionEfficiency.py',
+
+        # Library processing:
+        'singlecellmultiomics/libraryProcessing/libraryStatistics.py',
+        'singlecellmultiomics/libraryProcessing/scsortchicstats.py',
+        'singlecellmultiomics/libraryDetection/archivestats.py',
+        'singlecellmultiomics/alleleTools/heterozygousSNPedit.py',
+        'singlecellmultiomics/libraryProcessing/scsortchicfeaturedensitytable.py',
+        'singlecellmultiomics/libraryProcessing/scsortchicqc.py',
+
+        # Feature conversion:
+        'singlecellmultiomics/features/exonGTFtoIntronGTF.py',
+
+        # Variants:
+        'singlecellmultiomics/variants/postProcessVariants.py',
+        'singlecellmultiomics/variants/vcfFilterAlleleFreq.py',
+        'singlecellmultiomics/variants/vcfMutProfiler.py',
+        'singlecellmultiomics/variants/plotCovariates.py',
+
+        # Trimming:
+        'singlecellmultiomics/fastqProcessing/trim_vasa.py',
+
+        'singlecellmultiomics/utils/bigWigDiff.py',
+        # Utility: (SGE wrapper)
+        'singlecellmultiomics/utils/submission.py',
+        'singlecellmultiomics/utils/ftp_upload.py',
+
+        #Worfklow
+        'singlecellmultiomics/snakemake_workflows/scmo_workflow.py',
+        'singlecellmultiomics/snakemake_workflows/_general/sge_wrapper.py',
+        'singlecellmultiomics/snakemake_workflows/_general/slurm_wrapper.py',
+
+        # Facs:
+        'singlecellmultiomics/FACS/trajectory.py'
+
+        ],
+
+  install_requires=[
+       'pysam>=0.19.1','numpy>=1.16.5','pandas>=1.3.0','colorama','pyBigWig',
+       'cutadapt>=2.9',
+       'pysamiterators>=1.9','more-itertools','matplotlib','tabulate',
+       'wheel','setuptools>=40.8.0','scikit-learn>=0.21.3','seaborn>=0.11.2', 'statsmodels', 'cached_property',
+       'biopython>=1.71','pytest>=5.0.0','pytest-runner','snakemake>=5.8.1','lxml',
+       'statsmodels' #,'tensorflow>=1.14.0'
+   ],
+    setup_requires=["pytest-runner"],
+    tests_require=["pytest"],
+
+    include_package_data=True,
+
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Science/Research',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+         'License :: OSI Approved :: MIT License'
+        ]
+)