Note
We are in the process of packaging the system in a docker container to achieve a more reproducible, environment-independent local deployment solution. In the meantime please see our guidelines below which summarie necessary components and steps to run bio.tools.
The source code of the registry is under standard GPL 3.0 license and is available from https://github.com/bio-tools/biotoolsRegistry/.
The architecture of the registry is designed around the principle of decoupling frontend from the backend in order to eliminate performance bottlenecks at scale. The backend serves the data through the RESTful APIs which are in turn consumed by the the frontend SPA (Single-Page Application). The main advantage of this paradigm is that the frontend uses the exact same API calls that any user can invoke in order to create their own customized interface. The overall goal of scalability can be achieved by hosting the components independently (master database, replicated cache layer and static frontend code in a CDN - Content Delivery Network - such as Cloudflare or Akamai).
You only need Docker to run bio.tools locally.
The local (development) installation is done via Docker. Other than Git (and a text editor), nothing else is required to run and write code for bio.tools.
https://docs.docker.com/install/
Note
You will need to create a Docker Hub account.
Windows
https://docs.docker.com/docker-for-windows/install/
Note
Read the "What to know before you install" information to see if Docker Destktop for Windows can be installed on your system. If your system does not meet the requirements to run Docker Desktop for Windows, you can install the legacy Docker Toolbox.
MacOS
https://docs.docker.com/docker-for-mac/install/
CentOS
https://docs.docker.com/install/linux/docker-ce/centos/
Debian
https://docs.docker.com/install/linux/docker-ce/debian/
Fedora
https://docs.docker.com/install/linux/docker-ce/fedora/
Ubuntu
https://docs.docker.com/install/linux/docker-ce/ubuntu/
git clone https://github.com/bio-tools/biotoolsRegistry.git
git clone [email protected]:bio-tools/biotoolsRegistry.git
Go into the folder in which you cloned the bio.tools repo. By default it will be called biotoolsRegistry: (e.g. cd biotoolsRegistry or cd /home/user/coding/biotoolsRegistry )
Note
The Docker setup will require up to 5 GB of disk space. The bio.tools data will also add to this.
docker-compose build
The above command will download / build all the Docker images required for bio.tools to run on your local machine.
The images built can be seen by running: docker image ls and are:
biotools/frontend(~ 827MB)biotools/backend(~ 1.12GB)mysql(~ 205MB)(will show up after running 3.0.2)elasticsearch(~ 486MB)(will show up after running 3.0.2)python(~ 925MB)node(~ 650MB)
docker-compose up
The above command will create and run the required containers:
biotools-mysqlbiotools-elasticsearchbiotools-backend(depends onbiotools-mysqlandbiotools-elasticsearch)biotools-frontend(depends onbiotools-backend)
Note
After running the docker-compose up command, the containers will start and will output log messages which you can see in your terminal window. In order for the containers to keep running this window needs to stay open. You will need to open new terminal windows/tabs for other operations.
docker-compose up will also build the images if they do not exist, but in order to be sure your latest source code and image changes are running make sure you run docker-compose build beforehand
Too see the running containers run: docker container ls
Run the steps below in the root folder of the Git project (e.g. biotoolsRegistry )
docker exec biotools-backend python manage.py makemigrations
Make Django migrations from the exiting models. Executed on the biotools-backend container. If you get the No changes detected message it means that you are up to date.
docker exec biotools-backend python manage.py migrate
Create necessary tables and other DB objects from the migrations. Executed on the biotools-backend container. If you get the No migrations to apply. message it means that you are up to date.
docker cp initial_db.sql biotools-mysql:/root
Copies the initial_db.sql SQL file into the biotools-mysql container (where the MySQL database server runs) into the /root folder.
docker cp load_initial_db.sh biotools-mysql:/root
Copies the load_initial_db.sh into the biotools-mysql container. This file will run the MySQL commands used to load the database described in initial_db.sql
docker exec biotools-mysql bash /root/load_initial_db.sh
Executes the load_initial_db.sh file in the biotools-mysql container which loads the initial (seed) DB data.
Note
The initial DB contains 11 tool annotations, a superuser (username: biotools, password: biotools), an initial test subdomain and the necessary EDAM files. See 3.1.8 for more.
docker exec biotools-backend python manage.py es_purge
Purges (clears) any data in the Elasticsearch index. Executed in the biotools-backend container which communicates with the biotools-elasticsearch container.
docker exec biotools-backend python manage.py es_regenerate
Takes all the tools, subdomains annotations etc. in the DB and creates the equivalent entries in the Elasticsearch index. Executed in the biotools-backend container.
At this point you can go to http://localhost:8000 to see the local bio.tools homepage.
The test subdomain can be viewed at http://test.localhost:8000
You can login with the existing superuser (user: biotools, password: biotools).
All running Docker containers can be stopped by running: docker-compose down from the root Git folder. This will preserve the data in the MySQL database and Elasticsearch. To reinstantiate everything again run: docker-compose up.
Only need to run docker-compose build once at the beginning or if changes are made to the bio.tools Docker settings files.
If you wish to remove the data along with the containers run: docker-compose down -v which will also remove the Docker volumes which preserve the MySQL and Elasticsearch data.
This is an alternative to 3.1 in which some of the steps were contained in the initial DB files. This will start with no data.
Run the steps below in the root folder of the Git project (e.g. biotoolsRegistry )
docker exec biotools-backend python manage.py makemigrations
Make Django migrations from the exiting models. Executed on the biotools-backend container.
docker exec biotools-backend python manage.py migrate
Create necessary tables and other DB objects from the migrations. Executed on the biotools-backend container.
docker exec -it biotools-backend python manage.py createsuperuser
Prompts the creation of a superuser, need to input superuser name, email (optional) and password. Executed on the biotools-backend container.
docker exec biotools-backend bash /elixir/application/backend/data/edam/update_edam.sh
Download EDAM ontology and push it to the DB. Can also be used to update to new EDAM version. The file which indicates the EDAM version is <git_project_root>/backend/data/edam/current_version.txt, e.g. biotoolsRegistry/backend/data/edam/current_version.txt
docker cp update_site_settings.sql biotools-mysql:/root
Copies the update_site_settings.sql SQL file into the biotools-mysql container (where the MySQL database server runs) into the /root folder. This file contains SQL instructions used to create helper tables and settings for the project.
docker cp update_site_settings.sh biotools-mysql:/root
Copies the update_site_settings.sh into the biotools-mysql container. This file will run the MySQL commands described in update_site_settings.sql
docker exec biotools-mysql bash /root/update_site_settings.sh
Executes the update_site_settings.sh file in the biotools-mysql container which loads the helper tables and settings in the DB.
docker exec biotools-backend python manage.py es_purge
Purges (clears) any data in the Elasticsearch index. Executed in the biotools-backend container which communicates with the biotools-elasticsearch container.
docker exec biotools-backend python manage.py es_regenerate
Takes all the tools, subdomains annotations etc. in the DB and creates the equivalent entries in the Elasticsearch index. Executed in the biotools-backend container.
At this point you can go to http://localhost:8000 to see the local bio.tools homepage.
Login with the user created in 3.2.3
No tools or subdomains are available, add tools at http://localhost:8000/register and subdomains at http://localhost:8000/subdomain
All running Docker containers can be stopped by running: docker-compose down from the root Git folder. This will preserve the data in the MySQL database and Elasticsearch. To reinstantiate everything again run: docker-compose up.
Only need to run docker-compose build once at the beginning or if changes are made to the bio.tools Docker settings files.
If you wish to remove the data along with the containers run: docker-compose down -v which will also remove the Docker volumes which preserve the MySQL and Elasticsearch data.
After completing steps 1-3 above, the only required commands for basic use are
docker-compose up
and
docker-compose down
and perhaps
docker-compose down -v
After running docker-compose up you will see a number of log messages. These messages come from the running containers:
- biotools-mysql (MySQL logs)
- biotools-elasticsearch (Elasticsearch logs)
- biotools-backend (Mostly Apache logs, sometimes Python logs)
- biotools-frontend (Gulp logs)
The biotools-backend container is based on an image which uses an Apache server. The logs from biotools-backend come from Apache or sometimes from Python.
Note
Changes in Python/Django/backend files will be reflected in the biotools-backend container, BUT because of how Apache works, the changes won't be reflected in your browser http://localhost:8000 until Apache is reloaded. In order to see the changes in the reflected in the browser you need to run:
docker exec biotools-backend /etc/init.d/apache2 reload
Remember to run the above command whenever you want to see your code changes reflected in your local bio.tools.
Bringing the containers down and up agail will also work, but this takes significantly longer. The above command is almost instant.
Most issues with the backend code will be reflected in the browser at http://localhost:8000/api/{some_path}, e.g. http://localhost:8000/api/tool or http://localhost:8000/api/jaspar etc.
See https://biotools.readthedocs.io/en/latest/api_reference.html or Django route files (urls.py) for more API endpoints.
The biotools-frontend container outputs logs from gulp ( https://gulpjs.com/ ) which bundles all frontend JavaScript and CSS code.
Every time you change and save a .js or .css file in the frontend, gulp will re-bundle everything automatically. This implies that all changes in the frontend are reflected automatically in thr browser, unlike for the backend.
Note
If you have a syntax error in your JavaScript or CSS files, gulp will fail and you won't see any changes reflected in the browser. So, if your changes are not reflected, look at the biotools-frontend logs of gulp which will indicate if you made a syntax error in your code.
Similarly to section 3.2.4, in order to update to the latest EDAM version (or just use a different EDAM version) the update_edam.sh needs to be executed on the biotools-backend container.
The version number used for updating EDAM is specified in the file:
<git_project_root>/backend/data/edam/current_version.txt
In order to update to the latest EDAM version (e.g. 1.23) edit the current_version.txt file to store the value 1.23, save the file and run:
docker exec biotools-backend bash /elixir/application/backend/data/edam/update_edam.sh
The script file will download the specific EDAM version .owl file from https://github.com/edamontology/edamontology and execute the:
python /elixi/application/manage.py parse_edam
command in the biotools-backend container.
Note
The current_version.txt file is tracked by Git and any changes involving EDAM versions other than latest should not be pushed to the main branches of the repo.
Important to note that the email system used to send emails regarding account creation and password reset will not work as intended out of the box .
In order for the emails to work you need to provide credetials (email, password, smtp settings) in the backend/elixirapp/settings.py file. bio.tools production uses Zoho mail (http://zoho.com) which currently works well with our setup.
The easy way would be to make a Zoho email account and use that email information to make the email functionality run. Gmail and Yahoo were tried and the connections are blocked by Gmail and Yahoo because of security reasons. This is because Gmail and Yahoo don't accept a simple username-password login and require more strict settings. Feel free to implement this in your bio.tools instance.
docker-compose build
docker-compose up
docker-compose down
docker-compose down -v
docker container ls
docker container ls -a
docker container rm <CONTAINER_ID>
or
docker container rm <CONTAINER_ID1> <CONTAINER_ID2> <CONTAINER_ID3>
docker container rm -f <CONTAINER_ID>
or
docker container rm -f <CONTAINER_ID1> <CONTAINER_ID2> <CONTAINER_ID3>
docker container prune
docker image ls
docker image rm <IMAGE_ID>
or
docker image rm <IMAGE_ID1> <IMAGE_ID2> <IMAGE_ID2>
(will not work if containers are running this image)
Any of the bio.tools runnning containers can provide a bash terminal to run commands inside the containers (similar to docker exec). Examples of the commands are:
- docker exec -it biotools-mysql bash
- docker exec -it biotools-elasticsearch bash
- docker exec -it biotools-backend bash
- docker exec -it biotools-frontend bash
As an example, to view the info in a MySQL database table run:
docker exec -it biotools-mysql bash- In container:
mysql -u elixir -p(password is by default123) - In MySQL:
use elixir;
SELECT * FROM elixir_resource WHERE visibility = 1;
Backend build config file
<git_project_root>/backend/Dockerfile
Backend dockerignore file
<git_project_root>/backend/.dockerignore
Frontend build config file
<git_project_root>/frontend/Dockerfile
docker-compose YAML config file
<git_project_root>/docker-compose.yml
- https://docs.docker.com/
- https://docs.docker.com/reference/
- https://docs.docker.com/engine/reference/commandline/container/
- https://docs.docker.com/engine/reference/commandline/image/
- https://docs.docker.com/config/pruning/
- https://docs.docker.com/compose/
- https://hub.docker.com/
You can also check out our API instructions at the links below: