selection-atlas

Here be dragons.

Development docs:

• Implementation plan
• UI design
• Workflow design

Conda environment management

Assuming you have a recent version of mamba installed.

The file requirements.yml has the dependencies required to build the site. To ensure reproducibility we currently also maintain the file environment.yml which contains an export of the solved environment.

To create and activate an environment on your own computer:

mamba env create --force --file environment.yml
mamba activate selection-atlas

To create and activate an environment on datalab-bespin:

mamba env create --force --prefix=${HOME}/envs/selection-atlas --file environment.yml
conda activate ${HOME}/envs/selection-atlas

If you need to add or upgrade a package, edit requirements.yml. Do not edit environment.yml.

To upgrade environment.yml:

mamba env create --force --file requirements.yml
mamba env export -f environment.yml -n selection-atlas-requirements --override-channels --channel conda-forge --channel bioconda
sed -i "s/selection-atlas-requirements/selection-atlas/" environment.yml

Running the workflow

If running on your local system with GCS caching enabled, you'll need to run the build without any parallelisation:

snakemake -c1

If running on Google Cloud and GCS caching is disabled, you can try running with parallelisation, e.g.:

snakemake -c4