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 and BALSAMIC/conda/balsamic.yaml
  • Singularity >=version 3.0.0: BALSAMIC uses singularity to run vairous parts of the workflow. Either a container has to be built matching the BALSAMIC version from BALSAMIC/containers/Dockerfile.latest or one can pull Singularity

container from Docker using: singularity pull path_container_file docker://hassanf/balsamic:tag

  • Python 3.6

Manual Installation

  1. Create a conda environment using BALSAMIC/conda/balsamic.yaml:
conda env create --file BALSAMIC/conda/balsamic.yaml -n name_of_environment

You can also set conda environment prefix via --prefix option. Consult conda documentation for further instructions.

  1. Install BALSAMIC using pip within the newly created environment: pip install -r requirements.txt -e .
  2. Pull container using Singularity: singularity pull path_container_file docker://hassanf/balsamic

If you’d like to install release 5.0.0 the instruction will look like below:

# Checkout a specific tag or branch. If you'd like to install latest changes, use master branch
git checkout v5.0.0

# Create a conda env: balsamic_base
conda env create --file BALSAMIC/conda/balsamic.yaml --name balsamic_base

# Activate conda environment
source activate balsamic_base

# If you don't want to install in editable mode, remove `-e`
pip install -r requirements.txt -e .

# Pull container for release_v5.0.0
singularity pull balsamic_release_v5.0.0 docker://hassanf/balsamic:release_v5.0.0

Automatic Installation ~~~~~~~~~~~~~~~~~~~~~~3

NOTE: The following instructions are for internal use only.

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

./ -s S -p path_to_conda_env_location -P path_to_container_store_location -c

In above example, the final conda environment will be named: S_BALSAMIC

USAGE: ../ [-s _condaprefix -v _balsamic_ver -p _condapath -c]
  1. Conda naming convention: [P,D,S]_[ENVNAME]_%DATE. 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 to install (4.0.0+), or it could be the branch name
  -e _envsuffix       Balsamic conda env suffix. This will be added to the conda env name
  -p _condapath       Conda env path prefix. See point 2 in help above
  -P _containerpath   Container path to store container files. Default set to current directory
  -c                  If set it will use Singularity container for conda instead