This section describes steps to install BALSAMIC (version = 4.1.0)

Software Requirments

  • Conda >=version 4.5.0: For detailed software and python requirments please see requirments.txt and BALSAMIC/conda/balsamic.yaml

  • Singularity >=version 3.0.0: BALSAMIC uses singularity to run vairous parts of the workflow.

  • Python 3.6

Step 1. Installing BALSAMIC

  1. Create a conda environment:

conda create -c conda-forge -c defaults --name S_BALSAMIC python==3.7 pip
  1. Activate environment:

conda activate balsamic
  1. Install BALSAMIC using pip within the newly created environment:

pip install --no-cache-dir -U git+

Or if you have repository cloned and want it in editable mode:

pip install -e .

Step 2. generate BALSAMIC cache and pull containers

First generate your own COSMIC database key via: The following commands will create and download reference directory at ~/balsamic_cache (change this path if you want it to be created in another location):

NOTE: This process can take couple of hours

# Note:
# 1. COSMIC key is in variable $COSMIC_KEY
# 2. For genome version hg38, set --genome-version to hg38

balsamic init --outdir ~/balsamic_cache \
  --cosmic-key "${COSMIC_KEY}" \
  --genome-version hg19 \