# 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