diff --git a/README.md b/README.md
index b2647ccccc0494e3b724f6f60264365935adc473..0e3c428a1b3a4baf19b7ebdf7e9616063bedcaf2 100755
--- a/README.md
+++ b/README.md
@@ -6,9 +6,25 @@ They are based on the [Galaxy Genome Annotation (GGA) project](https://galaxy-ge
A stack of Docker services is deployed for each species, from an input yaml file describing the data.
See `examples/example.yml` for an example of what information can be described and the correct formatting of this input file.
+The services currently deployed are:
+- Chado database
+- Tripal: database interface and hub to all applications
+- Elasticsearch: searching service used in Tripal
+- JBrowse: genome browser
+- Nginx proxy: page to download the data files
+- Blast (optional): BLAST interface to query the data
+- Galaxy: data loading orchestrator for administrators
+
A GGA environment is deployed for each different species at [https://hostname/sp/genus_species/](https://hostname/sp/genus_species/).
Multiple strains can have the same species and are deployed in the same GGA environment.
+
+_**Figure** : Schematic representation of a set of Docker containers deployed with
+GGA for typical genomes. Cuboids represent Docker containers. Hexagons represent different
+sets of Docker containers. Blue arrows represent HTTP traffic. Gray arrows represent
+data exchange performed using Galaxy tools. Black arrows represent data exchange
+inherent in applications._
+
## Requirements
To run the gga_load_data tools, Python 3.6 and the packages listed in [requirements.txt](./requirements.txt) are required.
@@ -22,8 +38,8 @@ and a [swarm](https://docs.docker.com/engine/swarm/swarm-tutorial) (for cluster
Traefik is a reverse proxy which allows to direct HTTP traffic to various Docker Swarm services.
The Traefik dashboard is deployed at [https://hostname/traefik/](https://hostname/traefik/)
-Authelia is an authentication agent, which can be plugged to an LDAP server, and that Traefik can you to check permissions to access services.
-The authentication layer is optional. If used, the config file needs the variables `https_port`, `authentication_domain_name`, `authelia_config_path`.
+Authelia is an authentication agent, which can be plugged to an LDAP server, and that Traefik can used to check permissions to access services.
+The authentication layer is optional. If used, the config file needs the variables `https_port`, `authentication_domain_name`, `authelia_config_path`, `authelia_secrets_env_path`, `authelia_db_postgres_password`.
Authelia is accessed automatically by Traefik to check permissions everytime someones wants to access a page.
If the user is not logged in, he is redirected to the authelia portal.
diff --git a/constants.py b/constants.py
index 70724c3eb93de567dabf2855a0872c50bbb0cd83..2a50710854fd9409a9197fb0919d8f5da8630d6d 100644
--- a/constants.py
+++ b/constants.py
@@ -23,6 +23,7 @@ ORG_PARAM_DATA_OGS_VERSION = "ogs_version"
ORG_PARAM_DATA_PERFORMED_BY = "performed_by"
ORG_PARAM_SERVICES = "services"
ORG_PARAM_SERVICES_BLAST = "blast"
+ORG_PARAM_SERVICES_GO = "go"
# Constants used in the config yaml file
diff --git a/examples/citrus_sinensis.yml b/examples/citrus_sinensis.yml
index 63483e4e70dde45425a68185cf51ef18587ef403..38087bbe0cfe9b87dbd6519ddebd32730aab1dc7 100644
--- a/examples/citrus_sinensis.yml
+++ b/examples/citrus_sinensis.yml
@@ -18,7 +18,7 @@
# Paths to the different datasets to copy and import into the galaxy container (as a shared library)
# Must be absolute paths to the dataset
genome_path: /path/to/repo/examples/src_data/genome/v1.0/Citrus_sinensis-scaffold00001.fasta # Mandatory!
- transcripts_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta # Mandatory!
+ transcripts_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta
proteins_path: # Mandatory!
gff_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3 # Mandatory!
interpro_path: /path/to/repo/examples/src_data/annotation/v1.0/functional_annotation/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml
@@ -33,6 +33,6 @@
ogs_version: 1.0
performed_by:
services:
- # List the optional services to be deploy in the stack
- # By default, only tripal, tripaldb, galaxy, jbrowse and elasticsearch services will be deployed
- blast: 0
\ No newline at end of file
+ # List the optional services/resources to add
+ blast: 0 # "1" to add links to blast form, "some/url" to specify, multiple urls as "Name1=url1&Name2=url2", "0" to disable it. Default: "0"
+ go: 1 # "1" to add links to GO summary, "0" to disable it. Default: "0"
\ No newline at end of file
diff --git a/gga_init.py b/gga_init.py
index 6c2f7029bf9f7898deaf172f2303565406cfb9c3..a4fdb0139b9f593f887c1def9e8690e61b6fd7e8 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -130,7 +130,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
"genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name,
"genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species_lower(), self.sex),
"strain": self.strain, "sex": self.sex, "Genus_species": "{0} {1}".format(self.genus_uppercase, self.species_lower()),
- "blast": self.blast, "picture_path": self.picture_path}
+ "blast": self.blast, "go": self.go, "picture_path": self.picture_path}
if (len(self.config.keys()) == 0):
logging.error("Empty config dictionary")
# Merge the two dicts
diff --git a/images/gga_schema.png b/images/gga_schema.png
new file mode 100644
index 0000000000000000000000000000000000000000..c1b55fc01176684256778e2d408450d65d1c0a7d
Binary files /dev/null and b/images/gga_schema.png differ
diff --git a/speciesData.py b/speciesData.py
index 34c817fd23e93710c086b1534d0207730fcfc83f..d505da605add1aa724505b30a9973e919a05da80 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -47,12 +47,18 @@ class SpeciesData:
else:
return string
+ def set_service_attribute(self, attribute, service, parameters_dictionary):
+ parameters_dictionary_services = parameters_dictionary[constants.ORG_PARAM_SERVICES]
+ if(service in parameters_dictionary_services.keys()):
+ attribute = parameters_dictionary_services[service]
+ else:
+ attribute = "0"
+
def __init__(self, parameters_dictionary):
self.parameters_dictionary = parameters_dictionary
self.name = parameters_dictionary[constants.ORG_PARAM_NAME]
parameters_dictionary_description=parameters_dictionary[constants.ORG_PARAM_DESC]
parameters_dictionary_data = parameters_dictionary[constants.ORG_PARAM_DATA]
- parameters_dictionary_services = parameters_dictionary[constants.ORG_PARAM_SERVICES]
self.species = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_SPECIES])
self.genus = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_GENUS])
@@ -83,10 +89,8 @@ class SpeciesData:
self.blastx_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_BLASTX_PATH]
self.orthofinder_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_ORTHOFINDER_PATH]
- if(constants.ORG_PARAM_SERVICES_BLAST in parameters_dictionary_services.keys()):
- self.blast = parameters_dictionary_services[constants.ORG_PARAM_SERVICES_BLAST]
- else:
- self.blast = "0"
+ self.set_service_attribute(self.blast, constants.ORG_PARAM_SERVICES_BLAST, parameters_dictionary)
+ self.set_service_attribute(self.go, constants.ORG_PARAM_SERVICES_GO, parameters_dictionary)
if constants.ORG_PARAM_DESC_PICTURE_PATH in parameters_dictionary_description.keys():
self.picture_path = parameters_dictionary_description[constants.ORG_PARAM_DESC_PICTURE_PATH]
diff --git a/templates/gspecies_compose.yml.j2 b/templates/gspecies_compose.yml.j2
index 97dbb0000bcf779a9f6667d5376d24f888c096be..1b1e8f8f692ff0d745dc27448c196bd3dd1ba617 100644
--- a/templates/gspecies_compose.yml.j2
+++ b/templates/gspecies_compose.yml.j2
@@ -65,7 +65,7 @@ services:
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
diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2
index 9a05ccfc4c8abfee341532cf0e2464714a8882cc..019fce089740ba1634b15f2756f8d04e5fa2e5f3 100644
--- a/templates/organisms.yml.j2
+++ b/templates/organisms.yml.j2
@@ -23,4 +23,5 @@
{{ org_param_data_ogs_version }}: {{ org_param_data_ogs_version_value }}
{{ org_param_data_performed_by }}: {{ org_param_data_performed_by_value }}
{{ org_param_services }}:
- {{ org_param_services_blast }}: {{ org_param_services_blast_value }}
\ No newline at end of file
+ {{ org_param_services_blast }}: {{ org_param_services_blast_value }}
+ {{ org_param_services_go }}: {{ org_param_services_go_value }}
\ No newline at end of file
diff --git a/utilities.py b/utilities.py
index f08c11b25b25d1e4a65eeb2685acc68f987c01f1..bcee45e1c931fc5330951ecbad078089d27e6181 100755
--- a/utilities.py
+++ b/utilities.py
@@ -236,5 +236,6 @@ def create_org_param_dict_from_constants():
org_param_dict["org_param_data_performed_by"] = constants.ORG_PARAM_DATA_PERFORMED_BY
org_param_dict["org_param_services"] = constants.ORG_PARAM_SERVICES
org_param_dict["org_param_services_blast"] = constants.ORG_PARAM_SERVICES_BLAST
+ org_param_dict["org_param_services_go"] = constants.ORG_PARAM_SERVICES_GO
return org_param_dict