ABiMS theme for Tripal
Written for use with 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), multiple urls as "Name1=url1&Name2=url2", 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"