CCB

This repo contains a set of general functions for performing everyday ccb'ing

Maintained by Christopher Anderson and Jeff Smith

building the singularity container

Build the ccb singularity container using the ccb-singularity.build script.

# clone the latest version of the repo
git clone https://github.com/stanford-ccb/ccb.git
cd ccb/

# add the path to this repo as an environment variable
export CCB=$PWD
echo 'export CCB=$PWD' >> ~/.bashrc

# then build the singularity container into the bin directory
sudo singularity build bin/ccb ccb-singularity.build

# and add ccb/bin to your local path so you can easily access the container
export PATH=$CCB/bin:$PATH
echo 'export PATH=$CCB/bin:$PATH' >> ~/.bashrc

You can add then access the binary commands though the singularity container by typing e.g. ccb gbif-to-vector -h. You could also access the python module through e.g. ccb ipython then import ccb.