species compose update

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/