## Before You Start, Read This The purpose of this repo is to provide the steps for processing raw fq files for [Shotgun Sequencing Libraries - SSL Pipeline](https://github.com/philippinespire/pire_ssl_data_processing) for the [lcWGS Shotgun Sequencing Libraries - lcWGS Pipeline](https://github.com/philippinespire/pire_lcwgs_data_processing/tree/main) or for probe development and the [Capture Shotgun Sequencing Libraries- CSSL Pipeline](https://github.com/philippinespire/pire_cssl_data_processing). Scripts with `ssl` in the name are designed for shotgun data, including the `ssl` and `lcwgs` pipelines. Scripts with `cssl` in the name are designed for capture-shotgun data. Scripts with no suffix in the name can be used for both types of data. Both the `pire_ssl_data_processing` and `pire_cssl_data_processing` and `pire_lcwgs_data_processing` repos assume that the `pire_fq_gz_processing` repo is in the same directory as they are. ---

## Use Wahab We encourage everybody to use `wahab.hpc.odu.edu` or `turing.hpc.odu.edu`, preferably wahab. You can start by logging onto wahab ```bash ssh YourUserName@wahab.hpc.odu.edu ``` There are shared repos on wahab and turing in `/home/e1garcia/shotgun_PIRE` that you are encouraged to use. ```bash cd /home/e1garcia/shotgun_PIRE ``` If, however, you know that you deliberately don't want to use the shared repos on wahab and turing in `/home/e1garcia/shotgun_PIRE`, then here is how you would get started on another hpc and realize that you will have to modify all of the paths given in these `README.md` and tutorials. **ONLY DO THE FOLLOWING STEPS 0 AND 1 IF YOU ARE NOT USING WAHAB OR TURING** 0. Create a directory for your PIRE repos to live in, and cd into it ```bash mkdir cd ``` 1. Clone the repos into your PIRE working dir ```sh #cd to your working dir then git clone https://github.com/philippinespire/pire_fq_gz_processing.git # then choose which repo you are using git clone https://github.com/philippinespire/pire_ssl_data_processing.git git clone https://github.com/philippinespire/pire_cssl_data_processing.git git clone https://github.com/philippinespire/pire_lcwgs_data_processing.git ``` ---

## Git etiquette You must constantly be pulling and pushing changes to github with `git` or else you're going to mess up the repo. 1. Goto your PIRE working dir (`/home/e1garcia/shotgun_PIRE` on wahab) and use the `pire_fq_gz_processing` repo along with either `pire_ssl_data_processing` or `pire_cssl_data_processing` or `pire_lcwgs_data_processing`, and immediately start by pulling changes from github in the repos you are using **EACH TIME YOU LOG IN** ```bash # on wahab replace with /home/e1garcia/shotgun_PIRE cd /pire_fq_gz_processing git pull # replace with either ssl or cssl or lcwgs, no spaces cd /pire__data_processing git pull ``` 2. When your session is done, i.e. you are about to log off, push your changes to github **EACH TIME YOU LOG OUT** ```bash cd /pire__data_processing git pull # if there are no errors, then proceed, otherwise get help git add --all # if there are no errors, then proceed, otherwise get help git commit -m "insert message here" # if there are no errors, then proceed, otherwise get help git push ``` 3. As you work through this tutorial it is assumed that you will be running scripts from either `pire_ssl_data_processing` or `pire_cssl_data_processing` or `pire_lcwgs_data_processing` and you will need to add the path to the `pire_fq_gz_processing` directory before the script's name in the code blocks below. ```sh #add this path when running scripts on wahab #/pire_fq_gz_processing/