COBLE Installation

Installation can be done through conda or github.

Conda Installation

# In your chosen conda environment, or in base:
conda install rachelsa::coble
# Test it
coble -h

When installed through conda, the utility and all the scripts are in the path so you can refer to it as coble wherever you are.

Requirements

COBLE is a high-level bash utility that uses other package managers to build environments. It requires bash, conda, R and python to be installed and accessible from the command line as needed. It also has the option to use docker, and singularity/apptainer. These are all referred to by triggering the relevant package manager commands from bash and if you have alternative installations you can alias the executables.

To install conda

We recommend the miniforge version in conda-forge which defaults to the conda-forge channel: install miniforge

The .bashrc

The utility is not tied to conda, you can use any executable you like by passing the --alias setting. This means that rather than handle all the possible inits for hooks for the different package managers, COBLE sources the ~./bashrc, so it is there that you need to ensure that your package manager has the necessary hooks.

Generally this accomplished by following the install instructions which will end up with somethin glike conda init and the instruction to resstart your shell.

# In your ~/.bashrc
# For conda and mamba installed through conda
source "$(conda info --base)/etc/profile.d/conda.sh"
# For mamba (standalone):
eval "$(mamba shell hook --shell=bash)"
# For micromamba (standalone):
eval "$(micromamba shell hook --shell=bash)"

Thake care that your mamba and conda init are not interactive only. This would be signalled by a block like this:

# If not running interactively, don't do anything
case $- in
    *i*) ;;
      *) return;;
esac

which can be commented out.

Github installation

git clone git@github.com:coble-tools/coble.git
# Test it, and you can also test/(find the help for) each of the child commands:
coble/code/coble -h
coble/code/coble recipe -h
coble/code/coble build -h

You need to add the folder coble/code to the path or refer to the coble utility script by full or relative path.