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:
conda create -c conda-forge -c defaults --name S_BALSAMIC python==3.7 pip
Activate environment:
conda activate S_BALSAMIC
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 $COSMIC_KEY
# 2. For genome version hg38, set --genome-version to hg38
balsamic init --outdir ~/balsamic_cache \
--cosmic-key "${COSMIC_KEY}" \
--genome-version hg19 \
--run-analysis