Installation¶
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
andBALSAMIC/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¶
- Create a conda environment using
BALSAMIC/conda/BALSAMIC-base.yaml
- Install BALSAMIC using
pip
within the newly created environment:pip install -r requirements.txt -e .
- Pull container using Singularity:
singularity pull docker://hassanf/balsamic path_to_balsamic_container
Automatic Installation¶
Use install.sh
script, assuming ${CONDA_ENVS_PATH} is set to the path for conda environment:
./install.sh -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: ./install.sh [-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