Skip to content

bioinformatics-ua/biodata-starter-kit-se-deployment-notes

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

4 Commits
 
 
 
 

Repository files navigation

Biodata Starter Kit SE Deployment Guide

This guide outlines the procedure to deploy the GDI Starter Kit on a Biodata node (Portuguese GDI node). The deployment was executed on a single Virtual Machine (VM), utilizing Docker containers for deploying services.

System Requirements

  • A Virtual Machine (VM) running CentOS Linux release 7.9.2009.

Prerequisites

Before initiating the deployment process, some software must be installed. Detailed installation instructions can be found at:

Repositories Required for Deployment

The deployment utilizes several repositories, each offering different components for the overall system. You'll need to use the following repositories:

  1. Starter Kit Storage and Interfaces - This repository provides the required storage components and interfaces for the deployment.

  2. Starter Kit HTSget - This repository includes the component for data retrieval.

  3. Starter Kit REMS - This repository manages access rights to resources for the starter kit.

  4. Starter Kit Containerized Computation - This repository provides the components for containerized computation, essential for processing genomic data.

  5. Starter Kit Beacon2 RI API - This repository contains the Beacon v2 for the starter kit.

Deployment Procedure

Follow the steps provided below to successfully deploy the GDI Starter Kit:

Certificate Generation for Services

All user-facing services operate with TLS encryption for secure communication. We utilize Certbot to create these certificates. These certificates are stored in a Docker volume, which is mounted across all the containers.

To generate the certificates, run the following command:

sudo certbot certonly --standalone --noninteractive --agree-tos --preferred-challenges http --email jorge.miguel.ferreira.silva@ua.pt -d htsget.gdi.biodata.pt -d login.gdi.biodata.pt -d download.gdi.biodata.pt -d beacon.gdi.biodata.pt -d inbox.gdi.biodata.pt -d rems.gdi.biodata.pt --expand

sudo certbot certonly --standalone --noninteractive --agree-tos --preferred-challenges http --email [user]@[domain] \
-d htsget.gdi.biodata.pt \
-d login.gdi.biodata.pt \
-d download.gdi.biodata.pt \
-d beacon.gdi.biodata.pt \
-d inbox.gdi.biodata.pt \
-d rems.gdi.biodata.pt \
--expand

Important: Ensure that port 80 is open on your machine when running the command above.

(Add detailed deployment instructions here)

Note

Bear in mind, the deployment process can vary based on system specifications and configurations. For any issues or further assistance, please refer to our troubleshooting section.

Troubleshooting

(Add troubleshooting notes and common issues along with their solutions here)

Note: This guide assumes that you have basic understanding of Virtual Machines, Docker containers, and CentOS. If you are not familiar with these topics, we recommend reviewing relevant resources before proceeding.

About

Documentation of deployment of the GDI starter kit in Portuguese node

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published