Installation#

This section describes steps to install BALSAMIC (version = 15.0.1)

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 vairous parts of the workflow.

  • Python 3.11

  • BALSAMIC is dependent on third-party bioinformatics software Sentieon-tools. Example: for running wgs variant calling using TNScope, and to execute UMIworkflow.

Note: Set Sentieon envionment variables in your ~/.bashrc file by adding following two lines

export SENTIEON_INSTALL_DIR=path_to_sentieon_install_dir
export SENTIEON_LICENSE=IP:Port

Step 1. Installing BALSAMIC#

  1. Create a conda environment:

conda create -c conda-forge -c defaults --name S_balsamic python==3.11 pip pygraphviz wkhtmltopdf

  1. Activate environment:

conda activate S_BALSAMIC

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

pip install --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/help/file_download 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"