Alternative Strategies for Running PROseq_etal

An alternative way to run PROseq_etal is to clone the PROseq_etal repo locally. This makes updating PROseq_etal a bit of a hassle, as it is non-trivial to pull any updates from the PROseq_etal repo if you edited the config file. That being said, clonging the full repo can be useful if you need to make changes to the workflow due to idiosyncracies in your particular data. Therefore, this section discusses how to run PROseq_etal in this way.

Clone the PROseq_etal repository to wherever you would like on your system. You will eventually be navigating to this repo directory in the terminal and running Snakemake from inside the directory, so make sure your chosen location is conducive to this. Navigate to the directory in the terminal and run:

$ git clone https://github.com/isaacvock/PROseq_etal.git
$ cd PROseq_etal

You should be in the PROseq_etal repo directory now!

Step 1 of the Snakedeploy route (i.e., installing mamba/conda) is also the same for the Activating --use-conda and Running all rules inside one environment routes.

PROseq_etal is compatible with Snakemake's --use-conda option. This will cause Snakemake to automatically create and activate conda environments for each step of the workflow to run inside. If you want to use this functionality, you can start by creating a simple conda environment that contains snakemake, as such:

mamba create -c conda-forge -c bioconda --name snakemake snakemake

You would then run the pipeline with the snakemake environment activated with:

snakemake cores all --use-conda

where cores all is a convenient way to tell Snakemake to make use of all available cpus (all can be replaced with an explicit number as was shown in the installation/pipeline running instructions above).