This for starting the development environment. No deployment tools such as nginx or gunicorn are installed.

Some of the packages are required for a more specific task. For example, elasticsearch require installation of elastic search package and its dependencies. The main application is still functional without it. But the related searching function will be missing.

In the folder you want to save the application, pull repository from git using git, or download and unzip to that folder. Then change directory to that folder.

$ cd /path/to/your/folder
$ git clone https://github.com/rocksnow1942/ngs_server.git
$ cd ngs_server 
$ ls 

You should be able to see this:

Aptitude_NGS.py		certs			server_mapping
README.md		config.py		testNGSdbdata.py
Ubuntu Deploy Configs	fastq_tools.py
app			requirements.txt

The following command create a subfolder 'venv' and put python files in there. Then activate the virtual environment.

$ python -m venv venv 
$ source venv/bin/activate 

After this you should see (venv) in front of your terminal prompt.

Also, if you enter which python in terminal, you should see /path/to/your/folder/ngs_server/venv/bin/python. This means virtual environment is activated.

Then install all dependencies. All dependencies are installed to the venv folder.

$ pip install -r requirements.txt

No errors should occur. If you see error "xcrun: error: invalid active developer path", run

$ xcode-select --install 

to install the xcode tools. Then run the above command again.

The mysql server I tested with is 5.7.27. Any 5.7 mysql server version should work fine.

Download and install from MySQL Community Downloads.

After install, log in mysql with root and create user name and password. By default, root password is set to empty after install .

Then create a database called 'ngs' and new user 'ngs_server_user' to use this database.

$ sudo mysql -u root 
> create database ngs character set utf8mb4 collate utf8mb4_unicode_ci;
> create user 'ngs_server_user'@'localhost' identified by 'ngs_server_password';
> grant all privileges on ngs.* to 'ngs_server_user'@'localhost';
> flush privileges;
> quit;

Create .env file under ngs_server folder. Put in the following content with proper changes inside "< >". It will be fine if some are not changed. Website should still be able to run.

SECRET_KEY=a_secret_key
DATABASE_URL=mysql+pymysql://ngs_server_user:ngs_server_password@localhost:3306/ngs?charset=utf8mb4
MAIL_SERVER=smtp.googlemail.com
MAIL_PORT=587
MAIL_USE_TLS=1
MAIL_USERNAME=<your gmail address if you want to use email function>
MAIL_PASSWORD=<your gmail password>
UPLOAD_FOLDER=</path/to/your/folder>/ngs_server/app/cache/file_upload
ANALYSIS_FOLDER=</path/to/your/folder>/ngs_server/app/cache/analysis_data
ALLOWED_EXTENSIONS={'txt', 'pdf', 'png', 'jpg', 'jpeg', 'gif','csv','sql'}
PAGE_LIMIT=10
ELASTICSEARCH_URL=""
FOLDOJO_FOLDER=</path/to/your/folder>/ngs_server/app/APPS/foldojo/static/cache
BOKEH_SECRET_KEY=<generated bokeh key, not necessary>
BOKEH_SIGN_SESSIONS=1
PPT_SOURCE_FOLDER=<PPT slides folder, this is for server indexing>
PPT_TARGET_FOLDER=<PPT slides snapshot folder, this is for server reading snapshots>
PPT_LOG_FILE=</path/to/your/folder>/ngs_server/app/tasks/ppt_log.txt 
APP_ERROR_LOG=</path/to/your/folder>/ngs_server/logs/APP_ERROR_LOG.txt
DATABASE_FOLDER=<path to mysql storage, for calculate database disk usage>
ANIMAL_DATA_PATH=<path to animal data, for display animal data> 

Create .flaskenv file under ngs_server folder. Put in the following cotent.

FLASK_APP=Aptitude_NGS.py

Initiate the database in mysql server by run:

$ flask db init 
$ flask db migrate 
$ flask db update

Some errors might occur:

• ImportError: cannot import name 'ViennaRNA' from 'app.utils.folding' (unknown location)

This is caused by the ViennaRNA package is missing in the git repository. Solve this by commenting out the first line in ngs_server/app/utils/folding/_structurepredict.py to avoid importing ViennaRNA package. This way, you won't see predicted structure on NGS sequence page. Other function should be intact.

• Error: No such command "db".

This could be caused by a few reasons.

1. Make sure you are at the top-level of ngs_server folder.
2. Run which flask. If you are not getting /path/to/your/folder/ngs_server/venv/bin/flask This means your virtual environment is not active. Try restart the terminal, cd to the ngs_server folder, then run source venv/bin/activate again.

After you successfully initialize the database using flask db init, you will be able to lauch the applicaiton by running:

$ flask run 

If everything goes right, you should see:

* Serving Flask app "Aptitude_NGS.py"
* Environment: production
WARNING: This is a development server. Do not use it in a production deployment.
Use a production WSGI server instead.
* Debug mode: off
* Running on http://127.0.0.1:5000/ (Press CTRL+C to quit) 

Then you can access the applicaiton on http://127.0.0.1:5000/ in your browser.

All error information or print() information will be displayed in the terminal window during using the website.

The website is up, but you still need a user name and password to login.

Quit the applicaiton by CTRL + C. Then run:

$ flask shell 

This starts a python interactive session to talk with the backend. All database bindings are provided. You can create new user here.

> newuser = user(username = 'admin',privilege='admin') 
> newuser.set_password('admin')
> db.session.add(newuser)
> db.session.commit()

Then you can login with 'admin' / 'admin'.

Search function using elasticsearch is missing.

Apps rely on bokeh server is not able to load.