Collection of random helper functions and scripts, mostly for image analysis.

1. Install snakemake. See Snakemake's official documentation for details. Please install version 7.32.4 but not 8.0.0 or later, which should still be compatible with the pipelines in this repo but the instructions of how to run the pipelines are different.

2. Have snakemake create the conda environments for you on a node with internet access.

   snakemake -s {path/to/Snakefile} \
       --use-conda \
       --conda-prefix {path/to/automatically/created/envs} \
       -c1 all_envs
   

   We generally don't use --conda-create-envs-only when we want to install all dependencies ahead of time, independent of if certain rules have become discoverable (e.g., if they are after a checkpoint). But for simpler pipelines without checkpoints and if all_env is not provided, --conda-create-envs-only is a good option. Or, simply let snakemake create the conda environments on the fly if the pipeline is meant to be run entirely on a node with internet access.