Installation#

This section describes steps to install BALSAMIC (version = 19.0.0)

Software Requirements#

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

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

  • Python 3.11

  • BALSAMIC is dependent on third-party bioinformatics software Sentieon-tools for all workflows.

  • The BALSAMIC wrapper is hard-coded to the SLURM workload manager and requires scontrol

Note: To run Balsamic you need to supply the --sentieon-install-dir and --sentieon-license arguments during the config

Step 1. Installing BALSAMIC#

  1. Create a conda environment:

conda create --name S_balsamic -c conda-forge python=3.11 pip "cython<3" pygraphviz wkhtmltopdf snakemake-executor-plugin-slurm=1.7.0

  1. Activate environment:

conda activate S_BALSAMIC

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

pip install --no-build-isolation --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC

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: https://cancer.sanger.ac.uk/cosmic/register 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
# 3. For using develop container version, set --cache-version to develop
# 4. For submitting jobs to slurm cluster, use option --account

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

# Generate cache locally instead of slurm job submission
balsamic init --outdir ~/balsamic_cache \
  --cosmic-key "${COSMIC_KEY}" \
  --genome-version hg19 \
  --run-analysis \
  --run-mode local \
  --snakemake-opt "--cores 16"