README.md

# BIPAA theme for Tripal

Written for use with the ![the official tripal docker image](https://github.com/erasche/docker-tripal)

## Configuration

The theme can be configured using environment variables, which can be configured from the docker-compose.yml file.

```yaml
version: "2"
services:
  web:
    image: tripal:latest
    [...]
    environment:
      THEME_GIT_CLONE: "https://gitlab.inria.fr/abretaud/tripal_bipaa.git"
      THEME: "bipaa"
      SITE_NAME: "Spodoptera frugiperda" # Set this to the name of the species
      ENABLE_BLAST: 1 # 1 to add links to blast form, 0 to disable it
      ENABLE_JBROWSE: 1 # 1 to add links to jbrowse, 0 to disable it
      ENABLE_APOLLO: 1 # 1 to add links to apollo, 0 to disable it
      JBROWSE_LINKS: "SFRU_RICE>rice" # correspondance between contig name prefix and jbrowse dataset id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"
      # By default APOLLO_LINKS == JBROWSE_LINKS
      APOLLO_LINKS: "SFRU_RICE>rice" # correspondance between contig name prefix and apollo dataset id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"
    [...]
```