diff --git a/examples/config_example.yml b/examples/config_example.yml
index 21d0ac68b173a7f93f3b3e4aa621147ef8fecb09..795cd662b0934475260f0dc88a6556399bd93929 100644
--- a/examples/config_example.yml
+++ b/examples/config_example.yml
@@ -2,28 +2,28 @@
# "all" section contains variables used by several services at once or the paths to import sensitive files
all:
- hostname: localhost # The hosting machine name
- dashboard_port: 8001 # The desired port (on the hosting machine) for the traefik container dashboard
- http_port: 8888 # The HTTP port docker will use on the hosting machine
- https_port: 8889 # The HTTPS port docker will use on the hosting machine. Required for Authelia
- proxy_ip: XXXXXXXXXXXX # IP of the upstream proxy (used by Traefik)
- auth_hostname: XXXXXXXXXXXX # Required for Authelia. The authentication domain name.
+ hostname: localhost # Required. The hosting machine name
+ dashboard_port: 8001 # Required. The desired port (on the hosting machine) for the traefik container dashboard
+ 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
+ proxy_ip: XXXXXXXXXXXX # Required. IP of the upstream proxy (used by Traefik)
+ authentication_domain_name: XXXXXXXXXXXX # Required for Authelia. The authentication domain name.
authelia_config_path: /path/to/authelia_config.yml # Required for Authelia. Path to the Authelia configuration file
# galaxy-specific variables
galaxy:
- galaxy_default_admin_email: gga@galaxy.org
- galaxy_defaut_admin_user: gga
- galaxy_default_admin_password: password
- webapollo_user: admin_apollo@galaxy.org
- webapollo_password: apollopass
- galaxy_config_remote_user_maildomain: mydomain.com # The maildomain used by Galaxy authentication
- persist_galaxy_data: "True" # Optional. If True, docker data will be backed up. Do not set this variable to "false" for production
+ galaxy_default_admin_email: gga@galaxy.org # Required
+ galaxy_defaut_admin_user: gga # Required
+ galaxy_default_admin_password: password # Required
+ webapollo_user: admin_apollo@galaxy.org # Required
+ webapollo_password: apollopass # Required
+ galaxy_config_remote_user_maildomain: mydomain.com # Required. The maildomain used by Galaxy authentication
+ persist_galaxy_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
# tripal-specific variables
tripal:
- tripal_password: tripalpass # Tripal database password (also used by galaxy as an environment variable)
+ tripal_password: tripalpass # Required. Tripal database password (also used by galaxy as an environment variable)
banner_path: /my/path/banner.png # Optional. Custom banner path
tripal_theme_name: tripal_gga # Optional. Use this to use another theme
tripal_theme_git_clone: http://gitlab.sb-roscoff.fr/abims/e-infra/tripal_gga.git # Optional. Use this to install another theme.
# jbrowse-specific variables
jbrowse:
- menu_url: "http://localhost:8888/" # Used with run_workflow_phaeoexplorer.py. If present, this variable is used to define jbrowse menu_url, if absent, will use https://hostname:https_port instead
\ No newline at end of file
+ menu_url: "http://localhost:8888/" # Optional. Used with run_workflow_phaeoexplorer.py: if present, this variable is used to define JBrowse menu_url (to define the template url for the JBrowse feature's link to Tripal), if absent, will use default "https://hostname"
\ No newline at end of file
diff --git a/templates/authelia_users_template.yml b/files/authelia_users.yml
similarity index 100%
rename from templates/authelia_users_template.yml
rename to files/authelia_users.yml
diff --git a/templates/nginx_apollo.conf b/files/nginx_apollo.conf
similarity index 100%
rename from templates/nginx_apollo.conf
rename to files/nginx_apollo.conf
diff --git a/templates/nginx_download.conf b/files/nginx_download.conf
similarity index 100%
rename from templates/nginx_download.conf
rename to files/nginx_download.conf
diff --git a/gga_init.py b/gga_init.py
index 67be6ed92a25bdb6061838bcd3785143b0001c14..19aa31dc9dc5f93734df73c0afaba7b7f5d2e1b0 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -79,11 +79,10 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Create nginx dirs and write/re-write nginx conf
make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
try:
- with open(os.path.abspath("./nginx/conf/default.conf"), 'w') as conf:
- conf.write("server {\n\tlisten 80;\n\tserver_name ~.;\n\tlocation /download/ {\n\t\talias /project_data/; \n\t\tautoindex on;\n\t}\n}") # The species nginx conf
- except OSError as exc:
- logging.critical("Cannot edit NginX conf file")
- sys.exit(exc)
+ shutil.copy(os.path.join(self.script_dir, "files/nginx_download.conf"), os.path.abspath("./nginx/conf/default.conf"))
+ except Exception as exc:
+ logging.critical("Could not copy nginx configuration file for %s" % self.full_name)
+ logging.critical(exc)
# Return to main directory
os.chdir(self.main_dir)
@@ -107,7 +106,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Jinja2 templating, handled using the python "jinja2" module
file_loader = FileSystemLoader(self.script_dir + "/templates")
- env = Environment(loader=file_loader)
+ env = Environment(loader=file_loader, trim_blocks=True, lstrip_blocks=True)
# We need a dict holding all key (variables) - values that needs to be replaced in the template as our rendering dict
# To do so we need both input file vars and config vars
@@ -127,6 +126,14 @@ class DeploySpeciesStack(speciesData.SpeciesData):
gspecies_compose_file.truncate(0)
gspecies_compose_file.write(gspecies_compose_output)
+
+ galaxy_nginx_conf_template = env.get_template("galaxy_nginx.conf.j2")
+ galaxy_nginx_conf_output = galaxy_nginx_conf_template.render(render_vars)
+ with open(os.path.join(self.main_dir, "galaxy_nginx.conf"), "w") as galaxy_nginx_conf_file:
+ logging.debug("Writing the galaxy_nginx.conf file for %s" % self.genus_species)
+ galaxy_nginx_conf_file.truncate(0)
+ galaxy_nginx_conf_file.write(galaxy_nginx_conf_output)
+
# Create the volumes (directory) of the species docker-compose file
create_mounts(working_dir=".", main_dir=self.main_dir)
@@ -202,7 +209,7 @@ def make_traefik_compose_files(config, main_dir):
traefik_compose_file.truncate(0)
traefik_compose_file.write(traefik_compose_output)
- if config["authelia_config_path"]:
+ if "authelia_config_path" in config.keys():
if not config["authelia_config_path"] == "" or not config["authelia_config_path"] == "/path/to/authelia/config":
if os.path.isfile(os.path.abspath(config["authelia_config_path"])):
try:
@@ -217,11 +224,14 @@ def make_traefik_compose_files(config, main_dir):
# authelia_config_file.truncate(0)
# authelia_config_file.write(authelia_config_output)
else:
- logging.critical("Cannot find authelia configuration template path (%s)" % config["authelia_config_path"])
+ logging.critical("Cannot find authelia configuration path (%s)" % config["authelia_config_path"])
sys.exit()
+ else:
+ logging.critical("Invalid authelia configuration path (%s)" % config["authelia_config_path"])
+ sys.exit()
# Path to the authelia users in the repo
- authelia_users_path = script_dir + "/templates/authelia_users_template.yml"
+ authelia_users_path = script_dir + "/files/authelia_users_template.yml"
# Copy authelia "users" file
if not os.path.isfile("./traefik/authelia/users.yml"):
shutil.copy(authelia_users_path, "./traefik/authelia/users.yml")
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 3907a4396dca7e76d8efd612d4ec7673eb4616c3..49f3a2a9ba6ccab47bfd5e7118db987fee52d706 100755
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -492,9 +492,12 @@ class RunWorkflow(speciesData.SpeciesData):
# In case of the Jbrowse workflow, we unfortunately have to manually edit the parameters instead of setting them
# as runtime values, using runtime parameters makes the tool throw an internal critical error ("replace not found" error)
# Scratchgmod test: need "http" (or "https"), the hostname (+ port)
- # TODO --> use menu_url variable in config to set up the menu url
+ if "menu_url" not in self.config.keys():
+ jbrowse_menu_url = "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")
+ else:
+ jbrowse_menu_url = self.config["menu_url"]
if workflow_name == "Jbrowse":
- workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}"))
+ workflow_dict["steps"]["2"]["tool_state"] = workflow_dict["steps"]["2"]["tool_state"].replace("__MENU_URL__", jbrowse_menu_url)
# The UNIQUE_ID is specific to a combination genus_species_strain_sex so every combination should have its unique workflow
# in galaxy --> define a naming method for these workflows
workflow_dict["steps"]["3"]["tool_state"] = workflow_dict["steps"]["3"]["tool_state"].replace("__FULL_NAME__", self.full_name).replace("__UNIQUE_ID__", self.species_folder_name)
diff --git a/speciesData.py b/speciesData.py
index cf9da39cc8c1473f9d29c77b7f253cfb39c9be67..a2fcbdbfafabb742315fa73210b1c4f5fe102b7f 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -80,6 +80,7 @@ class SpeciesData:
self.datasets = dict()
self.config = None # Custom config used to set environment variables inside containers
self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase.lower(), self.species.lower(), self.strain.lower(), self.sex.lower()])["not_empty"])
+ self.species_folder_name = self.species_folder_name .replace("-", "_")
self.existing_folders_cache = {}
self.bam_metadata_cache = {}
diff --git a/templates/galaxy_nginx.conf.j2 b/templates/galaxy_nginx.conf.j2
new file mode 100644
index 0000000000000000000000000000000000000000..7920bef8618b3db8a9774549abc6f054d24ef1b0
--- /dev/null
+++ b/templates/galaxy_nginx.conf.j2
@@ -0,0 +1,18 @@
+uwsgi_param QUERY_STRING $query_string;
+uwsgi_param REQUEST_METHOD $request_method;
+uwsgi_param CONTENT_TYPE $content_type;
+uwsgi_param CONTENT_LENGTH $content_length;
+
+uwsgi_param REQUEST_URI $request_uri;
+uwsgi_param PATH_INFO $document_uri;
+uwsgi_param DOCUMENT_ROOT $document_root;
+uwsgi_param SERVER_PROTOCOL $server_protocol;
+uwsgi_param REQUEST_SCHEME $scheme;
+uwsgi_param HTTPS $https if_not_empty;
+
+uwsgi_param REMOTE_ADDR $remote_addr;
+uwsgi_param REMOTE_PORT $remote_port;
+uwsgi_param SERVER_PORT $server_port;
+uwsgi_param SERVER_NAME $server_name;
+
+uwsgi_param HTTP_REMOTE_USER {% if https_port is defined %}$http_remote_user if_not_empty;{% elif galaxy_defaut_admin_user is defined %}{{ galaxy_defaut_admin_user }};{% else %}$http_remote_user if_not_empty;{% endif %}
diff --git a/templates/gspecies_compose_template.yml.j2 b/templates/gspecies_compose_template.yml.j2
index 72e9595260f00de7e57b453475389fe92f56153c..d897fa2d99d52a30ca9d2dd20db081612b80900f 100644
--- a/templates/gspecies_compose_template.yml.j2
+++ b/templates/gspecies_compose_template.yml.j2
@@ -1,4 +1,3 @@
-#jinja2: lstrip_blocks: “Trueâ€, trim_blocks: "True"
# ./docker_data is created and filled with persistent data that should be backuped
version: '3.7'
services:
@@ -135,7 +134,6 @@ services:
galaxy:
image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod
volumes:
- - ../galaxy_data_libs_SI.py:/opt/galaxy_data_libs_SI.py
{% if persist_galaxy_data is defined %}
{% if persist_galaxy_data == "False" %}
#- ./docker_data/galaxy/:/export/
diff --git a/templates/traefik.yml b/templates/traefik.yml
deleted file mode 100644
index f47766c44505262e4709f5d6ca91e1a5fb4ecccd..0000000000000000000000000000000000000000
--- a/templates/traefik.yml
+++ /dev/null
@@ -1,120 +0,0 @@
-version: '3.7'
-services:
- traefik:
- image: traefik:2.1.6
- command:
- - "--api"
- - "--api.dashboard"
-# - "--api.insecure=true" # added by lg to debug, for dashboard
- - "--log.level=DEBUG"
- - "--providers.docker"
- - "--providers.docker.swarmMode=true"
- - "--providers.docker.network=traefikbig" # changed by lg from traefik to traefikbig
- - "--entryPoints.web.address=:80"
- - "--entryPoints.web.forwardedHeaders.trustedIPs=192.168.1.133" # The ips of our upstream proxies: eci
- - "--entryPoints.webs.address=:443"
- - "--entryPoints.webs.forwardedHeaders.trustedIPs=192.168.1.133" # The ips of our upstream proxies: eci
- ports:
- - 8001:8080 # added by lg to debug, for dashboard
- - 8888:80
- - 8889:443
- networks:
- - traefikbig
- volumes:
- - /var/run/docker.sock:/var/run/docker.sock
- deploy:
- placement:
- constraints:
- - node.role == manager
- labels:
-# - "traefik.http.routers.traefik-api.rule=PathPrefix(`/traefik`)"
- - "traefik.http.routers.traefik-api.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard`) || PathPrefix(`/traefik`)" # lg
-# - "traefik.http.routers.traefik-api.tls=true"
- - "traefik.http.routers.traefik-api.entryPoints=web" # lg
-# - "traefik.http.routers.traefik-api.entryPoints=webs"
- - "traefik.http.routers.traefik-api.service=api@internal"
- - "traefik.http.middlewares.traefik-strip.stripprefix.prefixes=/traefik"
- - "traefik.http.middlewares.traefik-auth.forwardauth.address=http://authelia:9091/api/verify?rd=https://auth.abims-gga.sb-roscoff.fr/"
- - "traefik.http.middlewares.traefik-auth.forwardauth.trustForwardHeader=true"
-# - "traefik.http.routers.traefik-api.middlewares=traefik-auth,traefik-strip"
- - "traefik.http.routers.traefik-api.middlewares=traefik-strip" # lg
- # Dummy service for Swarm port detection. The port can be any valid integer value.
- - "traefik.http.services.traefik-svc.loadbalancer.server.port=9999"
- # Some generally useful middlewares for organisms hosting
- - "traefik.http.middlewares.sp-auth.forwardauth.address=http://authelia:9091/api/verify?rd=https://auth.abims-gga.sb-roscoff.fr/"
- - "traefik.http.middlewares.sp-auth.forwardauth.trustForwardHeader=true"
- - "traefik.http.middlewares.sp-auth.forwardauth.authResponseHeaders=Remote-User,Remote-Groups"
-# - "traefik.http.middlewares.sp-trailslash.redirectregex.regex=^(https?://[^/]+/sp/[^/]+)$$"
- - "traefik.http.middlewares.sp-trailslash.redirectregex.regex=^(http?://[^/]+/sp/[^/]+)$$" # lg
- - "traefik.http.middlewares.sp-trailslash.redirectregex.replacement=$${1}/"
- - "traefik.http.middlewares.sp-trailslash.redirectregex.permanent=true"
-# - "traefik.http.middlewares.sp-app-trailslash.redirectregex.regex=^(https?://[^/]+/sp/[^/]+/[^/]+)$$"
- - "traefik.http.middlewares.sp-app-trailslash.redirectregex.regex=^(http?://[^/]+/sp/[^/]+/[^/]+)$$" # lg
- - "traefik.http.middlewares.sp-app-trailslash.redirectregex.replacement=$${1}/"
- - "traefik.http.middlewares.sp-app-trailslash.redirectregex.permanent=true"
- - "traefik.http.middlewares.sp-prefix.stripprefixregex.regex=/sp/[^/]+"
- - "traefik.http.middlewares.sp-app-prefix.stripprefixregex.regex=/sp/[^/]+/[^/]+"
- - "traefik.http.middlewares.tripal-addprefix.addprefix.prefix=/tripal"
- - "traefik.http.middlewares.sp-big-req.buffering.maxRequestBodyBytes=50000000"
- - "traefik.http.middlewares.sp-huge-req.buffering.maxRequestBodyBytes=2000000000"
- restart_policy:
- condition: on-failure
- delay: 5s
- max_attempts: 3
- window: 120s
-
- authelia:
- image: authelia/authelia:4.12.0
- networks:
- - traefikbig
- depends_on:
- - authelia-redis
- - authelia-db
- volumes:
- - ./authelia/:/etc/authelia/:ro
- deploy:
- labels:
- - "traefik.http.routers.authelia.rule=Host(`auth.example.org`)"
- - "traefik.http.services.authelia.loadbalancer.server.port=9091"
- restart_policy:
- condition: on-failure
- delay: 5s
- max_attempts: 3
- window: 120s
-
- authelia-redis:
- image: redis:5.0.7-alpine
- command: ["redis-server", "--appendonly", "yes"]
- volumes:
- - ./authelia-redis/:/data/
- networks:
- - traefikbig
- deploy:
- restart_policy:
- condition: on-failure
- delay: 5s
- max_attempts: 3
- window: 120s
-
- authelia-db:
- image: postgres:12.2-alpine
- environment:
- POSTGRES_PASSWORD: z3A,hQ-9
- volumes:
- - ./docker_data/authelia_db/:/var/lib/postgresql/data/
- networks:
- - traefikbig
- deploy:
- restart_policy:
- condition: on-failure
- delay: 5s
- max_attempts: 3
- window: 120s
-
-networks:
- traefikbig:
- driver: overlay
- name: traefikbig
- ipam:
- config:
- - subnet: 10.50.0.0/16
diff --git a/templates/traefik_compose_template.yml.j2 b/templates/traefik_compose_template.yml.j2
index 49fe94b2ec21fe8ff8750a4e534c16ee486eb74e..6157cc2acb31627e05c6b9105370980ea5b6ab3d 100644
--- a/templates/traefik_compose_template.yml.j2
+++ b/templates/traefik_compose_template.yml.j2
@@ -1,4 +1,3 @@
-#jinja2: lstrip_blocks: “Trueâ€, trim_blocks: "True"
version: '3.7'
services:
traefik:
@@ -89,7 +88,7 @@ services:
- ./authelia/:/etc/authelia/:ro
deploy:
labels:
- - "traefik.http.routers.authelia.rule=Host(`{{ auth_hostname }}`)"
+ - "traefik.http.routers.authelia.rule=Host(`{{ authentication_domain_name }}`)"
- "traefik.http.services.authelia.loadbalancer.server.port=9091"
restart_policy:
condition: on-failure