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. 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¶
- 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.
- Install BALSAMIC using
pip
within the newly created environment:pip install -r requirements.txt -e .
- 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 install.sh
script, assuming ${CONDA_ENVS_PATH} is set to the path for conda environment:
./install.sh -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: ../install.sh [-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