Release v2.1.0

General

• Bump cryptography requirement version to 3.2
• 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

templates/gspecies_compose.yml.j2

@@ -14,7 +14,7 @@ services:
           labels:
             # Download page
             - "traefik.http.routers.{{ genus_species }}-nginx.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/download`))"
-            {% if https_port is defined %}
+            {% if https_port is defined and https_port %}
             - "traefik.http.routers.{{ genus_species }}-nginx.tls=true"
             - "traefik.http.routers.{{ genus_species }}-nginx.entryPoints=webs"
             - "traefik.http.routers.{{ genus_species }}-nginx.middlewares=sp-auth,sp-app-trailslash,sp-prefix"
@@ -38,10 +38,18 @@ services:
             - ./docker_data/galaxy/:/export/:ro
             - ./src_data/:/project_data/:ro
             - ./src_data:/data:ro
-          {% if 'tripal_banner_path' is defined %}
+            {% if tripal_banner_path is defined and tripal_banner_path %}
             - ./banner.png:/var/www/html/banner.png:ro
-          {% endif %}
+            {% endif %}
             #- /groups/XXX/:/groups/XXX/:ro  # We do this when we have symlinks in src_data pointing to /groups/XXX/...
+            {% if picture_path is defined and picture_path %}
+                {% if 'png' in picture_path %}
+            - ./species.png:/var/www/html/species.png:ro
+                {% endif %}
+                {% if 'jpg' in picture_path %}
+            - ./species.jpg:/var/www/html/species.jpg:ro
+                {% endif %}
+            {% endif %}
         environment:
             DB_HOST: tripal-db.{{ genus_species }}
             BASE_URL_PATH: /sp/{{ genus_species }}
@@ -52,12 +60,13 @@ services:
             TRIPAL_ENABLE_MODULES: "tripal_analysis_blast tripal_analysis_interpro tripal_analysis_go tripal_rest_api tripal_elasticsearch"
             SITE_NAME: "{{ Genus_species }}"
             ELASTICSEARCH_HOST: elasticsearch.{{ genus_species }}
-            ENABLE_JBROWSE: /jbrowse/?data=data/{{ genus_species_strain_sex }}
+            ENABLE_JBROWSE: /jbrowse/?data=data/{{ jbrowse_dataset_id }}
+            JBROWSE_LINKS: {{ jbrowse_links }}
             ENABLE_APOLLO: 0
             ENABLE_BLAST: {{ blast }}
             ENABLE_DOWNLOAD: 1
             ENABLE_WIKI: 0
-            ENABLE_GO: 0
+            ENABLE_GO: {{ go }}
             ENABLE_ORTHOLOGY: 0
             ENABLE_ORTHOLOGY_LINKS: 0
             THEME: "{{ tripal_theme_name }}"  # Use this to use another theme
@@ -69,7 +78,7 @@ services:
         deploy:
           labels:
             - "traefik.http.routers.{{ genus_species }}-tripal.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}`))"
-            {% if https_port is defined %}
+            {% if https_port is defined and https_port %}
             - "traefik.http.routers.{{ genus_species }}-tripal.tls=true"
             - "traefik.http.routers.{{ genus_species }}-tripal.entryPoints=webs"
             - "traefik.http.routers.{{ genus_species }}-tripal.middlewares=sp-auth,sp-trailslash,sp-prefix,tripal-addprefix"
@@ -115,7 +124,7 @@ services:
     galaxy:
         image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod
         volumes:
-            {% if (galaxy_persist_data is defined) and (galaxy_persist_data == "False") %}
+            {% if (galaxy_persist_data is defined and galaxy_persist_data) and (galaxy_persist_data == "False") %}
             #- ./docker_data/galaxy/:/export/
             {% else %}
             - ./docker_data/galaxy/:/export/
@@ -133,8 +142,9 @@ services:
             GALAXY_CONFIG_USE_REMOTE_USER: "True"
             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_USER: "{{ galaxy_default_admin_user }}"
             GALAXY_DEFAULT_ADMIN_PASSWORD: "{{ galaxy_default_admin_password }}"
+            GALAXY_DEFAULT_ADMIN_KEY: "{{ galaxy_default_admin_key }}"
             GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org,{{ galaxy_default_admin_email }}"   # admin@galaxy.org is the default (leave it), galaxy_default_admin_email is a shared ldap user we use to connect
             ENABLE_FIX_PERMS: 0
             PROXY_PREFIX: /sp/{{ genus_species }}/galaxy
@@ -153,7 +163,7 @@ services:
         deploy:
           labels:
             - "traefik.http.routers.{{ genus_species }}-galaxy.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/galaxy`))"
-            {% if https_port is defined %}
+            {% if https_port is defined and https_port %}
             - "traefik.http.routers.{{ genus_species }}-galaxy.tls=true"
             - "traefik.http.routers.{{ genus_species }}-galaxy.entryPoints=webs"
             - "traefik.http.routers.{{ genus_species }}-galaxy.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
@@ -184,7 +194,7 @@ services:
         deploy:
           labels:
             - "traefik.http.routers.{{ genus_species }}-jbrowse.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/jbrowse`))"
-            {% if https_port is defined %}
+            {% if https_port is defined and https_port %}
             - "traefik.http.routers.{{ genus_species }}-jbrowse.tls=true"
             - "traefik.http.routers.{{ genus_species }}-jbrowse.entryPoints=webs"
             - "traefik.http.routers.{{ genus_species }}-jbrowse.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
@@ -199,7 +209,7 @@ services:
             max_attempts: 3
             window: 120s
 
-    {% if blast is defined and blast == 1 %}
+    {% if blast is defined and blast and blast == 1 %}
     blast:
         image: quay.io/abretaud/sf-blast:latest
         depends_on:
@@ -244,7 +254,7 @@ services:
         deploy:
           labels:
             - "traefik.http.routers.{{ genus_species }}-blast.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/blast`))"
-            {% if https_port is defined %}
+            {% if https_port is defined and https_port %}
             - "traefik.http.routers.{{ genus_species }}-blast.tls=true"
             - "traefik.http.routers.{{ genus_species }}-blast.entryPoints=webs"
             - "traefik.http.routers.{{ genus_species }}-blast.middlewares=sp-big-req,sp-auth,sp-app-trailslash,sp-app-prefix"