sangerpathogens/baker repository overview
baker
Baker is a tool that facilitates the installation and management of bioinformatics software. It leverages container technology such as singularity and docker as well as Jinja2 template to build wrapper scripts and singularity images
Install
Pip
Install master:
pip install git+https://github.com/sanger-pathogens/baker.git
Install a specific version:pip install git+https://github.com/sanger-pathogens/baker.git@<TAG>. Example:
pip install git+https://github.com/sanger-pathogens/[email protected]
Once install, baker can be run directly:
baker.py -h
Docker
Pull the latest image:
docker pull sangerpathogens/baker:latest
Run in a container:
docker run --rm -it -v /home:/home sangerpathogens/baker:latest baker.py -h
To pull and run a specific version, just replace latest by the version number. Example:
docker pull sangerpathogens/baker:0.0.1
docker run --rm -it -v /home:/home sangerpathogens/baker:0.0.1 baker.py -h
Usage
Please run baker.py -h for help
Legacy: building a singularity image based on templated singularity recipies
Use the vagrant file provided to build a box with necessary dependencies. Please ensure the singularity version is available in your target environment.
You can then execute as follow:
# Create a virtual environment and install baker:
virtualenv baker
source baker/bin/activate
pip install git+https://github.com/sanger-pathogens/[email protected]
# Create the necessary directory structure:
mkdir input templates output
# Copy the yaml files in input, the singularity templates in templates then execute
baker.py singularity legacy-bake -i ~/input -o ~/output -t ~/templates -n <image name>
# For example for paisnp 0.0.1=h6dfff17_0
baker.py singularity legacy-bake -i ~/input -o ~/output -t ~/templates -n pairsnp-0.0.1=h6dfff17_0.simg
License
Baker is free software, licensed under GPLv3.
Tag summary
Content type
Image
Digest
Size
201.6 MB
Last updated
almost 6 years ago
docker pull sangerpathogens/baker