Installation¶
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
andBALSAMIC/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¶
- Create a conda environment using
BALSAMIC/conda/balsamic.yaml
:
conda env create --file BALSAMIC/conda/balsamic.yaml --name balsamic
- Activate environment:
conda activate balsamic
- Install BALSAMIC using
pip
within the newly created environment:
pip install -r requirements.txt -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 $COSMIC_KEY
# 2. For genome version hg38, set --genome-version to hg38
balsamic init --outdir ~/balsamic_cache \
--cosmic-key "${COSMIC_KEY}" \
--genome-version hg19 \
--run-analysis