README 2.md

NeuroMabSeq Website

Just the website and database code install

Just the pipeline install

DJANGO + NGINX + GUNICORN see the tutorial for setup below.

1. Check out the Django Project Tutorial in this directory.

   • This will cover: (Look at files on the instance AMI for reference specifically NGINX.conf and Gunicorn.conf files)
   • https://www.digitalocean.com/community/tutorials/how-to-set-up-django-with-postgres-nginx-and-gunicorn-on-ubuntu-16-04

2. Setting Up the AWS instance and Mysql (Ubuntu 18.04)

   • ssh onto the instance (see private instructions) for the key and doing this in AWS -Setup of Mysql (no longer needed.. uses sqllite):

     sudo apt update
     sudo apt install mysql-server
     sudo mysql
     mysql> create database trimmer_lab;
     

   • sudo apt-get install mysql-devel (No longer needed, uses sqllite)

   • Django will want to connect using root user with no password to a local db.

     use mysql;
     update user set authentication_string=password(''), plugin='mysql_native_password' where user='root';
     

3. Conda setup

   • Setup of the conda:

     cd /tmp
     curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh
     bash Anaconda3-2019.03-Linux-x86_64.sh
     

     Yes ,yes ,yes enter etc. source ~/.bashrc
   • Setup of the conda env:

     conda env create --name trimmer_lab --file environment.yml
     source activate trimmer_lab
     

4. Repo setup

   • Setup the Repo

     git clone --single-branch --branch website https://github.com/ucdavis-bioinformatics/NeuroMabSeq.git
     

   • sudo apt-get install gcc

   • Run python manage.py runserver and see if it works along with python manage.py migrate, and python manage shell

5. Cert setup: https://certbot.eff.org/lets-encrypt/ubuntubionic-nginx

6. Adding users: https://aws.amazon.com/premiumsupport/knowledge-center/new-user-accounts-linux-instance/ (just steps)

7. Custom fasta renderer: https://www.django-rest-framework.org/api-guide/renderers/#custom-renderers

This will fix 99% of problems unless someone pushes something funny to the repo

sudo pkill gunicorn   
git fetch --all
git reset --hard origin/website_2.0
cd trimmer
python manage.py migrate
sudo systemctl restart gunicorn
sudo systemctl restart nginx
psudo python manage.py collectstatic

This will fix 99% of problems but will not update the repo

sudo pkill gunicorn   
sudo systemctl restart gunicorn
sudo systemctl restart nginx

Resetting the database: (see methods.py) need to make this stable for a login though (see ./reset_db.sh)

./manage.py shell < wipe_db.py
./manage.py shell < wipe_status_data.py
rm mydatabase
python manage.py migrate
./manage.py shell < run_update.py
./manage.py shell < run_status_update.py
./manage.py shell < run_metadata_update.py
./manage.py shell < run_metadata_update.py