Microbes Need Frenemies

Descriptions and code for metatranscriptome analysis related to project "Microbes need frenemies"

Eukrhythmic

Instructions for running eukrhythmic.

Running on HPC with slurm.

Followed all install instructions. See examples of set up documents, config.yaml and cluster.yaml for running snakemake workflow.

Use python submit scripts that come packaged with eukrhythmic. Using flag --np to perform dry run first.

conda activate eukrhythmic
python submit/eukrhythmic -np # to generate dry run, ensure everything runs ok.

# To run
python submit/eukrhythmic all

Local & remote workflow for data analysis

Make local changes

Add new changes to the git repo. Watch memory usage and keep large files separate. Add commit messages to annotate changes.

git add <newly-changed-files>
git commit -m "I changed my files!"

Return to remote:

Stay on branch on remote. But you can pull changes from main to your branch.

git pull origin main

Uploaded to a local staging area where you can render (For quarto github page) and keep modifying. When ready, push it to the main repository.

git push

Make changes remotely

First make sure local repo and remote are up to date.

git pull

You have the option to create a remote branch. Then merge the changes later.

git add <newly-changed-files>
git commit -m "I changed my files!"