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

Software Requirments

  • Conda: BALSAMIC requires conda 4.3+ for automated installation. For detailed

software and python requirments please see requirments.txt and BALSAMIC/conda/BALSAMIC-base.yaml

  • Singularity: BALSAMIC uses singularity to run vairous parts of the workflow. Either a container has to be built

matching the BALSAMIC version from BALSAMIC/containers/BALSAMIC.X.X.X or one can pull Singularity container from Docker using: singularity pull docker://hassanf/balsamic path_to_balsamic_container

  • Python 3.6

Manual Installation

  1. Create a conda environment using BALSAMIC/conda/BALSAMIC-base.yaml
  2. Install BALSAMIC using pip within the newly created environment: pip install -r requirements.txt -e .
  3. Pull container using Singularity: singularity pull docker://hassanf/balsamic path_to_balsamic_container

Automatic Installation

Use script, assuming ${CONDA_ENVS_PATH} is set to the path for conda environment:

./ -s D -v 3.2.2 -p ${CONDA_ENVS_PATH} -c

-s set prefix for conda environment name -v change the version tag or branch to append to env name -p path to conda environment location -c use conda 4.6.14 to install packages

In above example, the final conda environment will be named: D_BALSAMIC-base_3.2.2

USAGE: ./ [-s _condaprefix -v _balsamic_ver -p _condapath -c]
  1. Conda naming convention: [P,D,S]_[ENVNAME]_[balsamic_version_tag]. P: Production, D: Development, S: Stage
  2. Conda environment prefix: Path to conda env. e.g. /home/user/conda_env/

  -s _condaprefix  Conda env name prefix. This will be P or D in the help above
  -v _balsamic_ver Balsamic version tag or branch to install
  -p _condapath    Conda env path prefix. See point 2 in help above
  -c If set it will use Singularity container instead of local available conda