Paralogues plugin: install ensembl-compara

[nuno-agostinho]

Changelog

• Add ensembl-compara in INSTALL.pl
  • Required to create annotation for Paralogues plugin: ENSVAR-6290
  • Propagates to Docker image, as expected
• Build Docker image from context
  • Instead of remotely downloading Docker image, ensembl-vep repo is obtained from context (allowing us to easily test changes)
• Fix Docker build warnings
  • Change deprecated ENV var 2 to ENV var=2
  • Change to uppercase AS in FROM ubuntu:22.04 as builder

Documentation

• Add Docker command to Confluence docs; specific --file parameter and context location are now mandatory. Added to Manually build and push Docker image to DockerHub

Testing

1. Build Docker image inside the ensembl-vep repo¹:

   docker build . -t vep-compara -f docker/Dockerfile
   

2. Test if the ensembl-compara repo works by creating the Paralogues plugin annotation:

   docker run vep-compara \
     vep --id "4 89828156 rs201106962 A C" \
         --database --db_version 112 --force \
         --plugin Paralogues,clnsig=ignore
   

Footnotes

1. Building the Docker image in the docker folder won't allow to access files from the parent directory. These changes should work on the automatic build in GitHub Actions because it already takes into consideration the repo as the context: https://github.com/Ensembl/ensembl-vep/blob/main/.github/workflows/docker.yml#L43-L47 ↩

[likhitha-surapaneni]

Works as expected, thanks @nuno-agostinho

[likhitha-surapaneni]

Merged to main and release/113