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env.yaml
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name: yap
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python=3.8
- pip
- parallel
- jupyter
- snakemake
- mamba
- natsort
- anndata
- yaml
- biopython
- cutadapt=4.7
- bismark=0.20
- bowtie2
- bowtie
- samtools
- picard=3.1.1
- bedtools
- htslib
- pyBigWig
- ucsc-bedgraphtobigwig
- star=2.7.3a
- subread=2.0.1
- git
- ipython
- hdf5
- ipykernel
- graphviz
- fire
- papermill
- nbconvert-webpdf
- Black
- gdown=5.1.0
- scikit-learn=1.2.2
- pip:
# - nbconvert[webpdf]
- pybedtools==0.9.1
- pysam==0.20.0
- git+https://github.com/DingWB/cemba_data
- git+https://github.com/DingWB/ALLCools
- py-trello