# Conda configuration file to reproduce computing environment
#
# Create the conda environment:
#
# conda env create --file environment.yaml
#
# Update the conda environment:
#
# conda env update --file environment.yaml
#
# Activate the conda environment:
#
# source activate chromium
#
# Deactivate the conda environment:
#
# source deactivate chromium
#
# Resources:
name:
chromium
channels:
- bioconda
- conda-forge
- default
dependencies:
- deeptools
- picard
- subread
- pandoc
- fastqc
- snakemake
- umi_tools >= 0.5.1
- STAR >=2.7.3a-0
- samtools
- multiqc
- cutadapt
- pysam
- bcftools
- crossmap
- pandas
- numpy
- matplotlib
- r-essentials
- r-base
- r-optparse
- r-seurat
- bioconductor-dropletutils
- seqkit
- bedtools