diff --git a/templates/gspecies_compose_template.yml.j2 b/templates/gspecies_compose_template.yml.j2 index 0ef71b1b825ea5b39cbd23e1c0ba69af20074395..9963b5e866a41cd350315b8cd0f468cf57ad6b93 100644 --- a/templates/gspecies_compose_template.yml.j2 +++ b/templates/gspecies_compose_template.yml.j2 @@ -56,10 +56,22 @@ services: ENABLE_JBROWSE: /jbrowse/?data=data/{{ genus_species_sex }} # This ENABLE_JBROWSE variable should point to the "best assembly" by default --> tag it in the input file and use it to define this variable correctly (also called # unique id in the jbrowse tool parameters == both have to be identical) + {% if apollo == "True %} + ENABLE_APOLLO: 1 + {% else %} ENABLE_APOLLO: 0 + {% endif %} + {% if blast == "True" %} ENABLE_BLAST: 1 + {% else %} + ENABLE_BLAST: 0 + {% endif %} ENABLE_DOWNLOAD: 1 + {% if wiki == "True" %} + ENABLE_WIKI: 1 + {% else %} ENABLE_WIKI: 0 + {% endif %} ENABLE_GO: 0 ENABLE_ORTHOLOGY: 0 ENABLE_ORTHOLOGY_LINKS: 0 @@ -108,7 +120,7 @@ services: volumes: - ./docker_data/elastic_search_index/:/usr/share/elasticsearch/data/ environment: - bootstrap.memory_lock: "true" + # bootstrap.memory_lock: "true" xpack.security.enabled: "false" xpack.monitoring.enabled: "false" xpack.ml.enabled: "false" @@ -209,6 +221,7 @@ services: max_attempts: 3 window: 120s + {% if blast == "True" %} blast: image: quay.io/abretaud/sf-blast:latest depends_on: @@ -278,6 +291,7 @@ services: - ./docker_data/blast_db/:/var/lib/postgresql/data/ networks: - {{ genus_species }} + {% endif %} # wiki: # image: quay.io/abretaud/mediawiki