diff --git a/templates/gspecies_compose_template.yml.j2 b/templates/gspecies_compose_template.yml.j2 index bee4b2589ca3401a3ae5b3ee188d56356fc40919..ef300aeda3f80e24df88a5a0f821a3e7fe230926 100644 --- a/templates/gspecies_compose_template.yml.j2 +++ b/templates/gspecies_compose_template.yml.j2 @@ -136,7 +136,15 @@ services: image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod volumes: - ../galaxy_data_libs_SI.py:/opt/galaxy_data_libs_SI.py - #- ./docker_data/galaxy/:/export/ # Commented for testing TODO: Uncomment in production + {% if persist_galaxy_data is defined %} + {% if persist_galaxy_data == "False" %} + #- ./docker_data/galaxy/:/export/ + {% else %} + - ./docker_data/galaxy/:/export/ + {% endif %} + {% else %} + - ./docker_data/galaxy/:/export/ + {% endif %} - ./src_data/:/project_data/:ro #- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/... - ./docker_data/jbrowse/:/jbrowse/data/ @@ -148,12 +156,11 @@ services: GALAXY_CONFIG_BRAND: "{{ Genus }} {{ species }}" GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE: "True" GALAXY_CONFIG_USE_REMOTE_USER: "True" - GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "sb-roscoff.fr" + GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "{{ galaxy_config_remote_user_maildomain }}" GALAXY_DEFAULT_ADMIN_EMAIL: "{{ galaxy_default_admin_email }}" GALAXY_DEFAULT_ADMIN_USER: "{{ galaxy_defaut_admin_user }}" GALAXY_DEFAULT_ADMIN_PASSWORD: "{{ galaxy_default_admin_password }}" - GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org, gga@sb-roscoff.fr" # admin@galaxy.org is the default (leave it), gogepp@bipaa is a shared ldap user we use to connect - GALAXY_CONFIG_MASTER_API_KEY: "{{ galaxy_config_master_api_key }}" + GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org, {{ galaxy_default_admin_email }}" # admin@galaxy.org is the default (leave it), gogepp@bipaa is a shared ldap user we use to connect ENABLE_FIX_PERMS: 0 PROXY_PREFIX: /sp/{{ genus_species }}/galaxy GALAXY_TRIPAL_URL: http://tripal.{{ genus_species }}/tripal/