Github Setup

Create a fork of the https://github.com/rdalipo1/PFB-LOLA-seq repository

• Clone the ssh for you fork

git clone git@github.com:usr/fork_name.git

Make sure your fork is updated before pushing from your local

• Sync on the website
• Pull on local git pull

To contribute to the main, you need to push to your fork first, then contribute from the github website

• Push to your fork

git add
git commit -m 'message'
git push

• Contribute from fork github website

Development Setup

Create and activate a Python virtual environment with mamba:

$ mamba create -n lola-seq python=3.12
...
$ mamba activate lola-seq

Move to the top-level project directory and perform an "editable" install of the project:

$ cd PFB-LOLA-seq
PFB-LOLA-seq $ pip install -e .

This will install the project dependencies in the lola-seq virtual environment.

SRAToolkit Instructions

Download from mamba:

mamba activate lola-seq
mamba install -c bioconda -c conda-forge sra-tools=3.1.1

Instructions on how to use SRAtoolkit:

• Prefetch to grab the SRA file from NCBI: https://erilu.github.io/python-fastq-downloader/
• fastq-dump to convert SRA file to fastq: https://edwards.flinders.edu.au/fastq-dump/