Create tools to handle multiple docker stacks in docker_tools repository (toggl galaxy state, update service)
Input config.yml file
Fix typo in parameter galaxy_default_admin_user
Add parameter galaxy_default_admin_key (required to create the admin user galaxy_default_admin_user in Galaxy)
Check that all required parameters are not empty
Input organisms.yml file
Add the parameter picture_path in the description section to add this picture in the Tripal homepage
Add parameter contig_prefix in the data section to list the prefixes used for contig names. Required when they are multiple strains from the same species to map the contig name prefix to the right JBrowse dataset ID in Tripal (see Step "init")
Add the go summary functionality in Tripal. This functionality can be activated with parameter go set to 1 in the services section
Remove unused performed_by parameter
Fix code for empty strain and/or sex
Step "init"
Add a picture of the species in the Tripal homepage (the picture of the main strain if exists, the picture of another strain if not)
Fix Tripal site name
Add env variable JBROWSE_LINKS in the Tripal service, to map the contig name prefix to the right JBrowse dataset ID in Tripal (for Tripal hyperlinks to JBrowse)
Step "get data"
Change data file names: use prefix strain_sex
Step "run workflow Phaeoexplorer"
Create a parent module run_workflow_phaeo.py, with classes and methods used by the workflow scripts
Create file constants_phaeo.py to store constants used in step "run workflow Phaeoexplorer" (workflows and galaxy tools details)
Script gga_run_workflow_phaeo_jbrowse.py: runs a Galaxy workflow to load the genome, the annotations and the proteins to Chado, Tripal and JBrowse, for one or two strains of the same species
Work in progress: workflows to load blast and interpro results
# This is the configuration template file used by the gga_init.py, gga_load_data.py and run_workflow.py scripts
# These variables are used by several services at once or the paths to import sensitive files
hostname:localhost# Required. The hosting machine name
http_port:8888# Required. The HTTP port docker will use on the hosting machine
https_port:8889# Required for Authelia. The HTTPS port docker will use on the hosting machine
hostname:fancydb.com# Required. The hostname that will be used to access the application (http://hostname/sp/genus_species/)), possibly with a reverse proxy redirecting the requests to the host machine with the right port (http_port).
http_port:80# Required. The HTTP port docker will use on the hosting machine
https_port:443# Required for Authelia. The HTTPS port docker will use on the hosting machine
proxy_ip:XXX.XXX.XXX.XXX# Required. IP of the upstream proxy (used by Traefik)
authentication_domain_name:XXXXXXXX# Required for Authelia. The authentication domain name.
authentication_domain_name:auth.fancydb.com# Required for Authelia. The authentication domain name.
authelia_config_path:/path/to/authelia_config.yml# Required for Authelia. Path to the Authelia configuration file
authelia_secrets_env_path:/path/to/authelia/secrets.env# Required for Authelia. Path to the env file containing passwords and secrets needed for Authelia
authelia_db_postgres_password:XXXXXXXX# Required for Authelia.
authelia_db_postgres_password:psqlpwd# Required for Authelia.
galaxy_config_remote_user_maildomain:mydomain.com# Required. The maildomain used by Galaxy authentication
galaxy_persist_data:"True"# Optional (default: True). If False, docker data will NOT be persisted on your host's file system and will be lost any time the galaxy container is recreated. Do not set this variable to "False" for production
