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.
- A Virtual Machine (VM) running CentOS Linux release 7.9.2009.
Before initiating the deployment process, some software must be installed. Detailed installation instructions can be found at:
The deployment utilizes several repositories, each offering different components for the overall system. You'll need to use the following repositories:
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Starter Kit Storage and Interfaces - This repository provides the required storage components and interfaces for the deployment.
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Starter Kit HTSget - This repository includes the component for data retrieval.
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Starter Kit REMS - This repository manages access rights to resources for the starter kit.
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Starter Kit Containerized Computation - This repository provides the components for containerized computation, essential for processing genomic data.
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Starter Kit Beacon2 RI API - This repository contains the Beacon v2 for the starter kit.
Follow the steps provided below to successfully deploy the GDI Starter Kit:
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 [email protected] -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 \
--expandImportant: Ensure that port 80 is open on your machine when running the command above.
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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.
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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.