Installing

Pre-Installation recommendations

  1. Install conda if it has not been already using the conda install instructions.

  2. If ccanalyser is not being installed through conda, first generate a new conda environment using the yaml file in the GitHub repository:

conda env create -f ccanalyser_conda_env.yml
conda activate cc

  1. If you intend to use a cluster e.g. SunGrid engine/SLURM add the path to the DRMAA interface to your .bashrc:

# Access to the DRMAA library: https://en.wikipedia.org/wiki/DRMAA
echo "export DRMAA_LIBRARY_PATH=/<full-path>/libdrmaa.so" >> ~/.bashrc

# You can get this value from your configured environment:
env | grep DRMAA_LIBRARY_PATH

# or just look for the library:
find / -name "*libdrmaa.so"

Installation

The package can be installed in several ways:

Note

Currently only github installation is supported

1. Install from conda:

conda install ccanalyser # do not use: not available yet

2. Install from pypi:

pip install ccanalyser # do not use: not available yet

  1. Install from GitHub:

git clone https://github.com/sims-lab/capture-c.git
cd capture-c
pip install .