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Loraine Gueguen's avatar
Loraine Gueguen authored
Remove "other organisms are available at" on home page. Remove galaxy link. Add links to phaeo website and abims page "genomic resources"
d40d67ee

ABiMS theme for Tripal

Written for use with the the official tripal docker image

Configuration

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

version: "2"
services:
  web:
    image: tripal:latest
    [...]
    environment:
      THEME_GIT_CLONE: "http://gitlab.sb-roscoff.fr/abims/e-infra/tripal_abims.git"
      THEME: "abims"
      SITE_NAME: "Spodoptera frugiperda" # Set this to the name of the species
      ENABLE_BLAST: 1 # 1 to add links to blast form, some/url to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
      ENABLE_JBROWSE: 1 # 1 to add links to jbrowse, jbrowse?data=xxx to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
      ENABLE_APOLLO: 1 # 1 to add links to apollo, some/url to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
      ENABLE_DOWNLOAD: 1 # 1 to add links to download dir, some/url to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
      ENABLE_GO: 1 # 1 to add links to GO summary, some/url to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
      ENABLE_WIKI: 1 # 1 to add links to wiki, some/url to specify the path (relative to tripal BASE_URL_PATH), 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 organism id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"
    [...]

If you prefer, you can also use the organism abbreviation in JBROWSE_LINKS:

    JBROWSE_LINKS: "S. frugiperda corn>sfcorn;S. frugiperda rice>sfrice"