Streamline cBioPortal Docker Compose Initialization Setup

[zainasir]

Background:

• cBioPortal: cBioPortal is an open-source platform for cancer genomics data analysis and visualization. It provides a centralized resource for exploring and analyzing large-scale cancer genomic data sets, including genomic alterations, gene expression, and clinical information. The platform integrates data from multiple sources, including The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), and makes it available through a web interface for researchers, clinicians, and the general public. Please refer to the cBioPortal home page for an overview.
• Docker Compose: We also provide a Docker Compose Setup to allow users to spin up their own local instances of cBioPortal. This approach involves a lot of bash scripts that need to be run as part of the initialization setup, leading to incompatibility issues and silent errors when these scripts are run on varying operating systems.

Goal:

• Streamline the cBioPortal docker compose initialization setup by ensuring consistency across operating systems and eliminating silent errors.

Approach:

• Detect points of failure in the init scripts and eliminate them. Dockerize the init scripts to eliminate dependency on the operating system.
• Ensure the changes are backwards compatible.
• Test changes with other scripts in cbioportal-test repo and localdb tests

Need skills:
Familiarity with the command line, bash, docker/docker compose.

Possible mentors:
@zainasir

[Princekumarofficial]

@zainasir Indeed a great issue, It would be a great work to do, I love working with scripts, have explored it for a long time, will love to do this.
Also do you want to make some other minor fixes like
TODO: servlet-api should be excluded from deps in mvn, the removal below is just a quick fix

[NishchayRajput]

Hi @zainasir ,

I have few question in my mind.

1. Are there any know issues or some parts of the init script that have previously caused some problem?
2. Are there any existing discussions, issues, or resources you recommend looking into to better understand the scope of the improvements needed?