From dc2e8f3ae4a2b0e34e4e2b0a45bfcbb9fb35ff29 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Thu, 28 Jan 2021 09:45:39 +0100
Subject: [PATCH] jinja templating, more workflow changes, trying fixes for the
jbrowse gmod tool using API (in progress)
---
gga_init.py | 93 +++---
gga_load_data.py | 142 +-------
run_workflow_phaeoexplorer.py | 231 +++++++------
speciesData.py | 2 +-
templates/gspecies_compose_template.yml | 2 +-
templates/gspecies_compose_template.yml.j2 | 303 ++++++++++++++++++
templates/traefik_compose_template.yml.j2 | 120 +++++++
utilities.py | 11 +-
workflows/Chado_load_Tripal_synchronize.ga | 181 ++++++++---
.../Chado_load_Tripal_synchronize.ga.bak | 174 ++++++----
workflows/Jbrowse.ga | 12 +-
workflows/Jbrowse.ga.bak | 157 +++++++++
12 files changed, 1010 insertions(+), 418 deletions(-)
create mode 100644 templates/gspecies_compose_template.yml.j2
create mode 100644 templates/traefik_compose_template.yml.j2
create mode 100644 workflows/Jbrowse.ga.bak
diff --git a/gga_init.py b/gga_init.py
index 5a7b47d..8c5e507 100644
--- a/gga_init.py
+++ b/gga_init.py
@@ -11,7 +11,7 @@ import yaml
import shutil
from pathlib import Path
-from jinja2 import Template
+from jinja2 import Template, Environment, FileSystemLoader
import utilities
import speciesData
@@ -55,16 +55,15 @@ class DeploySpeciesStack(speciesData.SpeciesData):
sys.exit()
# Copy the custom banner to the species dir (banner used in tripal pages)
- if not self.config["custom_banner"] or not self.config["custom_banner"] == "/path/to/banner" or not self.config["custom_banner"] == "":
- try:
- logging.debug("Custom banner path: %s" % self.config["custom_banner"])
- if os.path.isfile(os.path.abspath(self.config["custom_banner"])):
- shutil.copy(os.path.abspath(self.config["custom_banner"]), "%s/banner.png" % self.species_dir)
-
- except FileNotFoundError:
- logging.warning("Specified banner not found (%s), skipping" % self.config["custom_banner"])
-
- # Copy nginx conf
+ # if not "custom_banner" not in self.config.keys() or not self.config["custom_banner"] == "/path/to/banner" or not self.config["custom_banner"] == "":
+ # try:
+ # logging.debug("Custom banner path: %s" % self.config["custom_banner"])
+ # if os.path.isfile(os.path.abspath(self.config["custom_banner"])):
+ # shutil.copy(os.path.abspath(self.config["custom_banner"]), "%s/banner.png" % self.species_dir)
+ # except FileNotFoundError:
+ # logging.warning("Specified banner not found (%s), skipping" % self.config["custom_banner"])
+
+ # Write nginx conf
try:
os.mkdir("./nginx/")
os.mkdir("./nginx/conf")
@@ -140,7 +139,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
sys.exit(0)
# Path to the templates used to generate the custom docker-compose files for an input species
- stack_template_path = self.script_dir + "/templates/gspecies_compose_template.yml"
+ gspecies_template_path = self.script_dir + "/templates/gspecies_compose_template.yml.j2"
traefik_template_path = self.script_dir + "/templates/traefik_compose_template.yml"
# authelia_config_path = self.script_dir + "/templates/authelia_config_example.yml" # Do not copy the authelia config!
authelia_users_path = self.script_dir + "/templates/authelia_users_template.yml"
@@ -154,31 +153,49 @@ class DeploySpeciesStack(speciesData.SpeciesData):
else:
genus_species_strain_sex = "{0}_{1}".format(self.genus.lower(), self.species)
- with open(stack_template_path, 'r') as infile:
- organism_content = list()
- for line in infile:
- # Replace placeholders in the compose file and append line to output
- organism_content.append(
- line.replace("genus_species",
- str(self.genus.lower() + "_" + self.species)).replace("Genus species",
- str(self.genus_uppercase + " " + self.species)).replace("Genus/species",
- str(self.genus_uppercase + "/" + self.species)).replace("gspecies",
- str(self.genus.lower()[0] + self.species)).replace("genus_species_strain_sex",
- genus_species_strain_sex))
- # Write/format the output compose file
- with open("./docker-compose.yml", 'w') as outfile:
- outfile.truncate(0) # Delete file content
- for line in organism_content: # Replace env variables by those in the config file
- for env_variable, value in self.config.items(): # env variables are stored in this dict
- # print("ENV VARIABLE: " + env_variable + "\t VALUE: " + value)
- if env_variable in line:
- line = line.replace(env_variable, value)
- break
- # Write the new line in the docker-compose
- outfile.write(line)
-
- # Create mounts for the current docker-compose
- self.create_mounts(working_dir=self.species_dir)
+ # with open(stack_template_path, 'r') as infile:
+ # organism_content = list()
+ # for line in infile:
+ # # Replace placeholders in the compose file and append line to output
+ # organism_content.append(
+ # line.replace("genus_species",
+ # str(self.genus.lower() + "_" + self.species)).replace("Genus species",
+ # str(self.genus_uppercase + " " + self.species)).replace("Genus/species",
+ # str(self.genus_uppercase + "/" + self.species)).replace("gspecies",
+ # str(self.genus.lower()[0] + self.species)).replace("genus_species_strain_sex",
+ # genus_species_strain_sex))
+ # # Write/format the output compose file
+ # with open("./docker-compose.yml", 'w') as outfile:
+ # outfile.truncate(0) # Delete file content
+ # for line in organism_content: # Replace env variables by those in the config file
+ # for env_variable, value in self.config.items(): # env variables are stored in this dict
+ # # print("ENV VARIABLE: " + env_variable + "\t VALUE: " + value)
+ # if env_variable in line:
+ # line = line.replace(env_variable, value)
+ # break
+ # # Write the new line in the docker-compose
+ # outfile.write(line)
+
+ # # Create mounts for the current docker-compose
+ # self.create_mounts(working_dir=self.species_dir)
+
+
+ # jinja templating, handled using the python jinja module (TODO: use ansible to handle the templating in production)
+ file_loader = FileSystemLoader(self.script_dir + "/templates")
+ env = Environment(loader=file_loader)
+ template = env.get_template("gspecies_compose_template.yml.j2")
+
+ # 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
+ # Create input file vars dict
+ input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
+ "genus_species": self.genus_species, "genus_species_strain_sex": self.full_name,
+ "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:]}
+ # Merge the two dicts
+ render_vars = {**self.config, **input_vars}
+ output = template.render(render_vars)
+
+ print(output)
try:
os.chdir(os.path.abspath(self.main_dir))
@@ -381,7 +398,7 @@ if __name__ == "__main__":
# Deploy the stack
logging.info("Deploying stack for %s..." % deploy_stack_for_current_organism.full_name)
- deploy_stack_for_current_organism.deploy_stack()
+ # deploy_stack_for_current_organism.deploy_stack()
logging.info("Successfully deployed stack for %s" % deploy_stack_for_current_organism.full_name)
logging.info("Stack deployed for %s" % deploy_stack_for_current_organism.full_name)
diff --git a/gga_load_data.py b/gga_load_data.py
index 25b8a65..fc214b1 100644
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -207,73 +207,6 @@ class LoadData(speciesData.SpeciesData):
return self.history_id
- # def import_datasets_into_history(self):
- # """
- # Find datasets in a library, get their ID and import thme into the current history if they are not already
-
- # :return:
- # """
-
- # # Instanciate the instance
- # gio = GalaxyInstance(url=self.instance_url,
- # email=self.config["custom_galaxy_default_admin_email"],
- # password=self.config["custom_galaxy_default_admin_password"])
-
- # prj_lib = gio.libraries.get_previews(name="Project Data")
- # self.library_id = prj_lib[0].id
-
- # instance_source_data_folders = self.instance.libraries.get_folders(library_id=str(self.library_id))
-
- # folders_ids = {}
- # current_folder_name = ""
- # # Loop over the folders in the library and map folders names to their IDs
- # for i in instance_source_data_folders:
- # for k, v in i.items():
- # if k == "name":
- # folders_ids[v] = 0
- # current_folder_name = v
- # if k == "id":
- # folders_ids[current_folder_name] = v
-
- # # Iterating over the folders to find datasets and map datasets to their IDs
- # logging.info("Datasets IDs: ")
- # for k, v in folders_ids.items():
- # if k == "/genome":
- # sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
- # final_sub_folder_content = self.instance.folders.show_folder(folder_id=sub_folder_content["folder_contents"][0]["id"], contents=True)
- # for k2, v2 in final_sub_folder_content.items():
- # for e in v2:
- # if type(e) == dict:
- # if e["name"].endswith(".fa"):
- # self.datasets["genome_file"] = e["ldda_id"]
- # logging.info("\t" + e["name"] + ": " + e["ldda_id"])
- # if k == "/annotation":
- # sub_folder_content = self.instance.folders.show_folder(folder_id=v, contents=True)
- # final_sub_folder_content = self.instance.folders.show_folder(folder_id=sub_folder_content["folder_contents"][0]["id"], contents=True)
- # for k2, v2 in final_sub_folder_content.items():
- # for e in v2:
- # if type(e) == dict:
- # # TODO: manage versions? (differentiate between the correct folders using self.config)
- # if "transcripts" in e["name"]:
- # self.datasets["transcripts_file"] = e["ldda_id"]
- # logging.info("\t" + e["name"] + ": " + e["ldda_id"])
- # elif "proteins" in e["name"]:
- # self.datasets["proteins_file"] = e["ldda_id"]
- # logging.info("\t" + e["name"] + ": " + e["ldda_id"])
- # elif "gff" in e["name"]:
- # self.datasets["gff_file"] = e["ldda_id"]
- # logging.info("\t" + e["name"] + ": " + e["ldda_id"])
-
- # logging.info("Uploading datasets into history %s" % self.history_id)
- # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["genome_file"])
- # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["gff_file"])
- # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["transcripts_file"])
- # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["proteins_file"])
-
- # return {"history_id": self.history_id, "library_id": self.library_id, "datasets": self.datasets}
-
-
-
def remove_homo_sapiens_from_db(self):
"""
Run the GMOD tool to remove the "Homo sapiens" default organism from the original database
@@ -303,80 +236,6 @@ class LoadData(speciesData.SpeciesData):
pass
- # def prepare_history(self):
- # """
- # Galaxy instance startup in preparation for importing datasets and running a workflow
- # - Remove Homo sapiens from the chado database.
- # - Add organism and analyses into the chado database --> separate
- # - Get any other existing organisms IDs before updating the galaxy instance --> separate
-
- # Calling this function is mandatory to have a working galaxy instance history
- # TODO Run a check to see if the instance is correctly set up
-
- # :return:
- # """
-
- # self.connect_to_instance()
- # self.set_get_history()
-
- # # Delete Homo sapiens from Chado database
- # logging.debug("Getting 'Homo sapiens' ID in instance's chado database")
- # get_sapiens_id_job = self.instance.tools.run_tool(
- # tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.2",
- # history_id=self.history_id,
- # tool_inputs={"genus": "Homo", "species": "sapiens"})
- # get_sapiens_id_job_output = get_sapiens_id_job["outputs"][0]["id"]
- # get_sapiens_id_json_output = self.instance.datasets.download_dataset(dataset_id=get_sapiens_id_job_output)
- # try:
- # logging.debug("Deleting Homo 'sapiens' in the instance's chado database")
- # get_sapiens_id_final_output = json.loads(get_sapiens_id_json_output)[0]
- # sapiens_id = str(
- # get_sapiens_id_final_output["organism_id"]) # needs to be str to be recognized by the chado tool
- # self.instance.tools.run_tool(
- # tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.2",
- # history_id=self.history_id,
- # tool_inputs={"organism": str(sapiens_id)})
- # except bioblend.ConnectionError:
- # logging.debug("Homo sapiens isn't in the instance's chado database")
- # except IndexError:
- # logging.debug("Homo sapiens isn't in the instance's chado database")
- # pass
-
- # # Add organism (species) to chado
- # logging.info("Adding organism to the instance's chado database")
- # self.instance.tools.run_tool(
- # tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_add_organism/organism_add_organism/2.3.2",
- # history_id=self.history_id,
- # tool_inputs={"abbr": self.abbreviation,
- # "genus": self.genus,
- # "species": self.species,
- # "common": self.common})
-
- # # Add OGS analysis to chado
- # logging.info("Adding OGS analysis to the instance's chado database")
- # self.instance.tools.run_tool(
- # tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2",
- # history_id=self.history_id,
- # tool_inputs={"name": self.genus + " " + self.species + " OGS" + self.ogs_version,
- # "program": "Performed by Genoscope",
- # "programversion": str("OGS" + self.ogs_version),
- # "sourcename": "Genoscope",
- # "date_executed": self.date})
-
- # # Add genome analysis to chado
- # logging.info("Adding genome analysis to the instance's chado database")
- # self.instance.tools.run_tool(
- # tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2",
- # history_id=self.history_id,
- # tool_inputs={"name": self.genus + " " + self.species + " genome v" + self.genome_version,
- # "program": "Performed by Genoscope",
- # "programversion": str("genome v" + self.genome_version),
- # "sourcename": "Genoscope",
- # "date_executed": self.date})
- # self.get_organism_and_analyses_ids()
- # logging.info("Finished initializing instance")
-
-
def purge_histories(self):
"""
Delete all histories in the instance
@@ -720,3 +579,4 @@ if __name__ == "__main__":
else:
logging.critical("The galaxy container for %s is not ready yet!" % load_data_for_current_species.full_name)
+ sys.exit()
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index c28a769..f3ca06e 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -18,7 +18,7 @@ from bioblend import galaxy
"""
gga_init.py
-Usage: $ python3 gga_init.py -i input_example.yml [OPTIONS]
+Usage: $ python3 gga_init.py -i input_example.yml --config [config file] [OPTIONS]
"""
@@ -34,20 +34,6 @@ class RunWorkflow(speciesData.SpeciesData):
"""
- # def get_species_history_id(self):
- # """
- # Set and return the current species history id in its galaxy instance
-
- # :return:
- # """
-
- # histories = self.instance.histories.get_histories(name=str(self.full_name))
- # self.history_id = histories[0]["id"]
- # self.instance.histories.show_history(history_id=self.history_id)
-
- # return self.history_id
-
-
def set_get_history(self):
"""
Create or set the working history to the current species one
@@ -125,17 +111,6 @@ class RunWorkflow(speciesData.SpeciesData):
return {"history_id": self.history_id, "library_id": self.library_id, "datasets": self.datasets}
- # def import_datasets_to_history(self):
- # """
- # Load the datasets into the current species history
- # OBSOLETE
- # """
- # logging.info("Uploading datasets into history %s" % self.history_id)
- # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["genome_file"])
- # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["gff_file"])
- # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["transcripts_file"])
- # self.instance.histories.upload_dataset_from_library(history_id=self.history_id, lib_dataset_id=self.datasets["proteins_file"])
-
def connect_to_instance(self):
"""
Test the connection to the galaxy instance for the current organism
@@ -143,18 +118,18 @@ class RunWorkflow(speciesData.SpeciesData):
"""
self.instance = galaxy.GalaxyInstance(url=self.instance_url,
- email=self.config["custom_galaxy_default_admin_email"],
- password=self.config["custom_galaxy_default_admin_password"]
+ email=self.config["galaxy_default_admin_email"],
+ password=self.config["galaxy_default_admin_password"]
)
- logging.info("Connecting to the galaxy instance...")
+ logging.info("Connecting to the galaxy instance %s" % self.instance_url)
try:
self.instance.histories.get_histories()
except bioblend.ConnectionError:
- logging.critical("Cannot connect to galaxy instance @ " + self.instance_url)
+ logging.critical("Cannot connect to galaxy instance %s" % self.instance_url)
sys.exit()
else:
- logging.info("Successfully connected to galaxy instance @ " + self.instance_url)
+ logging.info("Successfully connected to galaxy instance %s" % self.instance_url)
def prepare_history(self):
@@ -240,22 +215,20 @@ class RunWorkflow(speciesData.SpeciesData):
self.instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)
workflow_attributes = self.instance.workflows.get_workflows(name=workflow_name)
workflow_id = workflow_attributes[0]["id"]
- logging.debug("Workflow ID: %s" % workflow_id)
show_workflow = self.instance.workflows.show_workflow(workflow_id=workflow_id)
try:
- logging.info("Workflow ID: %s" % workflow_id)
+ logging.debug("Workflow ID: %s" % workflow_id)
except Exception:
- logging.warning("Error retrieving workflow attributes")
- logging.debug("Workflow ID: " + workflow_id)
+ logging.warning("Error retrieving workflow attributes for workflow %s" % workflow_name)
- logging.info("Running workflow: %s" % workflow_name)
self.instance.workflows.invoke_workflow(workflow_id=workflow_id,
history_id=self.history_id,
params=workflow_parameters,
inputs=datamap,
- inputs_by="")
+ inputs_by="",
+ allow_tool_state_corrections=True)
- # self.instance.workflows.delete_workflow(workflow_id=workflow_id) # TODO : Keep for prod? (add a "if test" condition)
+ logging.info("Successfully imported and invoked workflow {0}, check your galaxy instance ({1}) for the jobs state".format(workflow_name, self.instance_url))
def import_datasets_into_history(self):
"""
@@ -266,8 +239,8 @@ class RunWorkflow(speciesData.SpeciesData):
# Instanciate the instance
gio = GalaxyInstance(url=self.instance_url,
- email=self.config["custom_galaxy_default_admin_email"],
- password=self.config["custom_galaxy_default_admin_password"])
+ email=self.config["galaxy_default_admin_email"],
+ password=self.config["galaxy_default_admin_password"])
prj_lib = gio.libraries.get_previews(name="Project Data")
self.library_id = prj_lib[0].id
@@ -464,83 +437,133 @@ if __name__ == "__main__":
run_workflow_for_current_organism.config = utilities.parse_config(args.config)
# Set the instance url attribute
for env_variable, value in run_workflow_for_current_organism.config.items():
- if env_variable == "custom_host":
- run_workflow_for_current_organism.instance_url = "http://{0}:8888/sp/{1}_{2}/galaxy/".format(
- value, run_workflow_for_current_organism.genus_lowercase, run_workflow_for_current_organism.species)
+ if env_variable == "hostname":
+ run_workflow_for_current_organism.instance_url = "http://{0}:8888/sp/{1}/galaxy/".format(
+ value, run_workflow_for_current_organism.genus_species)
break
else:
run_workflow_for_current_organism.instance_url = "http://localhost:8888/sp/{0}_{1}/galaxy/".format(
run_workflow_for_current_organism.genus_lowercase,
run_workflow_for_current_organism.species)
- run_workflow_for_current_organism.connect_to_instance()
- run_workflow_for_current_organism.set_get_history()
- # run_workflow_for_current_organism.get_species_history_id()
+ # TODO: Create distinct methods to call different pre-set workflows using CL arguments/config options (i.e load-chado, jbrowse, functional-annotation, orthology, ...)
+
+ # If input workflow is Chado_load_Tripal_synchronize.ga
+ if "Chado_load_Tripal_synchronize" in str(workflow):
+
+ logging.info("Executing workflow 'Chado_load_Tripal_synchronize'")
+
+ run_workflow_for_current_organism.connect_to_instance()
+ run_workflow_for_current_organism.set_get_history()
+ # run_workflow_for_current_organism.get_species_history_id()
+
+ # Prepare the instance+history for the current organism (add organism and analyses in Chado) TODO: add argument "setup"
+ # (although it should pose no problem as the "Chado add" refuses to duplicate an analysis/organism anyway)
+ run_workflow_for_current_organism.prepare_history()
+
+ # Get the attributes of the instance and project data files
+ run_workflow_for_current_organism.get_instance_attributes()
+ run_workflow_for_current_organism.get_organism_and_analyses_ids()
+
+ # Import datasets into history
+ # TODO: it seems it is not required anymore since using "ldda" option for datasets in the workflow datamap doesn't need files from history
+ run_workflow_for_current_organism.import_datasets_into_history()
+
+ # Explicit workflow parameter names
+ GENOME_FASTA_FILE = "0"
+ GFF_FILE = "1"
+ PROTEINS_FASTA_FILE = "2"
+ TRANSCRIPTS_FASTA_FILE = "3"
+
+ LOAD_FASTA_IN_CHADO = "4"
+ LOAD_GFF_IN_CHADO = "5"
+ SYNC_ORGANISM_INTO_TRIPAL = "6"
+ SYNC_GENOME_ANALYSIS_INTO_TRIPAL = "7"
+ SYNC_OGS_ANALYSIS_INTO_TRIPAL = "8"
+ SYNC_FEATURES_INTO_TRIPAL = "9"
+
+ workflow_parameters = {}
+
+ workflow_parameters[GENOME_FASTA_FILE] = {}
+ workflow_parameters[GFF_FILE] = {}
+ workflow_parameters[PROTEINS_FASTA_FILE] = {}
+ workflow_parameters[TRANSCRIPTS_FASTA_FILE] = {}
+ workflow_parameters[LOAD_FASTA_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
+ "analysis_id": run_workflow_for_current_organism.genome_analysis_id,
+ "do_update": "true"}
+ # Change "do_update": "true" to "do_update": "false" in above parameters to prevent appending/updates to the fasta file in chado
+ # WARNING: It is safer to never update it and just change the genome/ogs versions in the config
+ workflow_parameters[LOAD_GFF_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
+ "analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
+ workflow_parameters[SYNC_ORGANISM_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
+ workflow_parameters[SYNC_GENOME_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
+ workflow_parameters[SYNC_OGS_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.genome_analysis_id}
+ workflow_parameters[SYNC_FEATURES_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
+
+ # Datamap for input datasets - dataset source (type): ldda (LibraryDatasetDatasetAssociation)
+ run_workflow_for_current_organism.datamap = {}
+ run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
+ run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
+ run_workflow_for_current_organism.datamap[PROTEINS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
+ run_workflow_for_current_organism.datamap[TRANSCRIPTS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
+
+ run_workflow_for_current_organism.datamap = {}
+ run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id":
+ run_workflow_for_current_organism.datasets["genome_file"]}
+ run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda",
+ "id": run_workflow_for_current_organism.datasets[
+ "gff_file"]}
+
+ # Run the Chado load Tripal sync workflow with the parameters set above
+ run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
+ workflow_parameters=workflow_parameters,
+ datamap=run_workflow_for_current_organism.datamap,
+ workflow_name="Chado load Tripal synchronize")
- # Prepare the instance+history for the current organism (add organism and analyses in Chado) TODO: add argument "setup"
- # (althought it should pose no problem as the "Chado add" refuses to duplicate an analysis/organism anyway)
- run_workflow_for_current_organism.prepare_history()
- # Get the attributes of the instance and project data files
- run_workflow_for_current_organism.get_instance_attributes()
- run_workflow_for_current_organism.get_organism_and_analyses_ids()
+ # Jbrowse creation workflow
+ elif "Jbrowse" in str(workflow):
- # Import datasets into history
- # TODO: put this only for the chado load tripal sync workflow?
- # TODO: it seems it is not required anymore since using "ldda" option for datasets in the workflow datamap doesn't need the files
- run_workflow_for_current_organism.import_datasets_into_history()
+ logging.info("Executing workflow 'Jbrowse'")
- # Explicit workflow parameter names
- # TODO: Create distinct methods to call different pre-set workflows using CL arguments/config options (i.e load-chado, jbrowse, functional-annotation, orthology, ...)
+ run_workflow_for_current_organism.connect_to_instance()
+ run_workflow_for_current_organism.set_get_history()
+ run_workflow_for_current_organism.get_instance_attributes()
+ run_workflow_for_current_organism.get_organism_and_analyses_ids()
+ run_workflow_for_current_organism.import_datasets_into_history()
- # Chado load and Tripal synchronize workflow
- workflow_parameters = {}
-
- GENOME_FASTA_FILE = "0"
- GFF_FILE = "1"
- PROTEINS_FASTA_FILE = "2"
- TRANSCRIPTS_FASTA_FILE = "3"
-
-
- LOAD_FASTA_IN_CHADO = "4"
- LOAD_GFF_IN_CHADO = "5"
- SYNC_ORGANISM_INTO_TRIPAL = "6"
- SYNC_GENOME_ANALYSIS_INTO_TRIPAL = "7"
- SYNC_OGS_ANALYSIS_INTO_TRIPAL = "8"
- SYNC_FEATURES_INTO_TRIPAL = "9"
-
- workflow_parameters[GENOME_FASTA_FILE] = {}
- workflow_parameters[GFF_FILE] = {}
- workflow_parameters[PROTEINS_FASTA_FILE] = {}
- workflow_parameters[TRANSCRIPTS_FASTA_FILE] = {}
- workflow_parameters[LOAD_FASTA_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
- "analysis_id": run_workflow_for_current_organism.genome_analysis_id,
- "do_update": "true"}
- # Change "do_update": "true" to "do_update": "false" in above parameters to prevent appending/updates to the fasta file in chado
- # WARNING: It is safer to never update it and just change the genome/ogs versions in the config
- workflow_parameters[LOAD_GFF_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
- "analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
- workflow_parameters[SYNC_ORGANISM_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
- workflow_parameters[SYNC_GENOME_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
- workflow_parameters[SYNC_OGS_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.genome_analysis_id}
- workflow_parameters[SYNC_FEATURES_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
-
- # Datamap for input datasets - dataset source (type): ldda (LibraryDatasetDatasetAssociation)
- run_workflow_for_current_organism.datamap = {}
- run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
- run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
- run_workflow_for_current_organism.datamap[PROTEINS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
- run_workflow_for_current_organism.datamap[TRANSCRIPTS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
-
- # Run the Chado load Tripal sync workflow with the parameters set above
- run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
- workflow_parameters=workflow_parameters,
- datamap=run_workflow_for_current_organism.datamap,
- workflow_name="Chado load Tripal synchronize")
+ GENOME_FASTA_FILE = "0"
+ GFF_FILE = "1"
+ ADD_JBROWSE = "2"
+ ADD_ORGANISM_TO_JBROWSE = "3"
+
+ workflow_parameters = {}
+
+ workflow_parameters[GENOME_FASTA_FILE] = {}
+ workflow_parameters[GFF_FILE] = {}
+ # Jbrowse custom feature url
+ workflow_parameters[ADD_JBROWSE] = {"jb_menu": {"menu_url": "http://{hostname}:{port}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=run_workflow_for_current_organism.config["hostname"],
+ port=run_workflow_for_current_organism.config["http_port"],
+ genus_sp=run_workflow_for_current_organism.genus_species,
+ Genus=run_workflow_for_current_organism.genus_uppercase,
+ species=run_workflow_for_current_organism.species,
+ id="id")}}
+ # Organism to add to the Jbrowse "container" (consists of a name and an id, not tied to the galaxy instance or chado/tripal names and ids)
+ workflow_parameters[ADD_ORGANISM_TO_JBROWSE] = {"name": [{"name": run_workflow_for_current_organism.full_name,
+ "unique_id": run_workflow_for_current_organism.abbreviation}]}
+
+ run_workflow_for_current_organism.datamap = {}
+ run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
+ run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
+
+ # Run the jbrowse creation workflow
+ run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
+ workflow_parameters=workflow_parameters,
+ datamap=run_workflow_for_current_organism.datamap,
+ workflow_name="Chado load Tripal synchronize")
- # Jbrowse creation workflow
- workflow_parameters = {}
else:
logging.critical("The galaxy container for %s is not ready yet!" % run_workflow_for_current_organism.full_name)
+ sys.exit()
diff --git a/speciesData.py b/speciesData.py
index 1e9305b..8e48cf5 100644
--- a/speciesData.py
+++ b/speciesData.py
@@ -40,7 +40,7 @@ class SpeciesData:
self.full_name_lowercase = self.full_name.lower()
self.abbreviation = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase[0], self.species, self.strain, self.sex])["not_empty"])
self.genus_species = self.genus_lowercase + "_" + self.species
- self.instance_url = "http://scratchgmodv1:8888/sp/" + self.genus_lowercase + "_" + self.species + "/galaxy/" # Testing with scratchgmodv1, is overwritten in the script by the provided hostname anyway
+ self.instance_url = "http://scratchgmodv1:8888/sp/" + self.genus_lowercase + "_" + self.species + "/galaxy/" # Testing with scratchgmodv1, is overwritten in the script by the provided hostname
self.instance = None
self.history_id = None
self.library = None
diff --git a/templates/gspecies_compose_template.yml b/templates/gspecies_compose_template.yml
index 1fe698f..da6d645 100644
--- a/templates/gspecies_compose_template.yml
+++ b/templates/gspecies_compose_template.yml
@@ -114,7 +114,7 @@ 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/
+ #- ./docker_data/galaxy/:/export/ # Commented for testing TODO: Uncomment in production
- ./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/
diff --git a/templates/gspecies_compose_template.yml.j2 b/templates/gspecies_compose_template.yml.j2
new file mode 100644
index 0000000..1111add
--- /dev/null
+++ b/templates/gspecies_compose_template.yml.j2
@@ -0,0 +1,303 @@
+# ./docker_data is created and filled with persistent data that should be backuped
+
+version: '3.7'
+services:
+ proxy:
+ image: quay.io/abretaud/nginx-ldap:latest
+ volumes:
+ - ./src_data/:/project_data/
+ #- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/...
+ - ./nginx/conf:/etc/nginx/conf.d
+ networks:
+ - traefikbig
+ - {{ genus_species }}
+ deploy:
+ labels:
+ # Download page
+ - "traefik.http.routers.{{ genus_species }}-nginx.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/download`))"
+# - "traefik.http.routers.{{ genus_species }}-nginx.tls=true"
+# - "traefik.http.routers.{{ genus_species }}-nginx.entryPoints=webs"
+ - "traefik.http.routers.{{ genus_species }}-nginx.entryPoints=web" # lg
+# - "traefik.http.routers.{{ genus_species }}-nginx.middlewares=sp-auth,sp-app-trailslash,sp-prefix"
+ - "traefik.http.routers.{{ genus_species }}-nginx.middlewares=sp-app-trailslash,sp-prefix" # lg
+ - "traefik.http.services.{{ genus_species }}-nginx.loadbalancer.server.port=80"
+ restart_policy:
+ condition: on-failure
+ delay: 5s
+ max_attempts: 3
+ window: 120s
+
+ tripal:
+ image: quay.io/galaxy-genome-annotation/tripal:v2.x
+ depends_on:
+ - tripal-db
+ - elasticsearch
+ volumes:
+ - ./docker_data/galaxy/:/export/:ro
+ - ./src_data/:/project_data/:ro
+ - ./src_data:/data:ro
+ - ./banner.png:/var/www/html/banner.png:ro
+ #- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/...
+ environment:
+ DB_HOST: tripal-db.{{ genus_species }}
+ BASE_URL_PATH: /sp/{{ genus_species }}
+ UPLOAD_LIMIT: 20M
+ MEMORY_LIMIT: 512M
+ TRIPAL_GIT_CLONE_MODULES: "https://github.com/abretaud/tripal_rest_api.git[@c6f9021ea5d4c6d7c67c5bd363a7dd9359228bbc] https://github.com/tripal/tripal_elasticsearch.git[@dc7f276046e394a80a7dfc9404cf1a149006eb2a] https://github.com/tripal/tripal_analysis_interpro.git https://github.com/tripal/tripal_analysis_go.git https://github.com/tripal/tripal_analysis_blast.git https://github.com/tripal/tripal_analysis_expression.git[@7240039fdeb4579afd06bbcb989cb7795bd4c342]"
+ TRIPAL_DOWNLOAD_MODULES: ""
+ 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_sex }}
+ ENABLE_APOLLO: 0
+ ENABLE_BLAST: 1
+ ENABLE_DOWNLOAD: 1
+ ENABLE_WIKI: 0
+ ENABLE_GO: 0
+ ENABLE_ORTHOLOGY: 0
+ ENABLE_ORTHOLOGY_LINKS: 0
+ THEME: "{{ tripal_theme_name }}" # Use this to use another theme
+ THEME_GIT_CLONE: "{{ tripal_theme_git_clone }}" # Use this to install another theme
+ ADMIN_PASSWORD: {{ tripal_password }} # You need to define it and update it in galaxy config below
+ networks:
+ - traefikbig
+ - {{ genus_species }}
+ deploy:
+ labels:
+ - "traefik.http.routers.{{ genus_species }}-tripal.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}`))"
+# - "traefik.http.routers.{{ genus_species }}-tripal.tls=true"
+# - "traefik.http.routers.{{ genus_species }}-tripal.entryPoints=webs"
+ - "traefik.http.routers.{{ genus_species }}-tripal.entryPoints=web" # lg
+# - "traefik.http.routers.{{ genus_species }}-tripal.middlewares=sp-auth,sp-trailslash,sp-prefix,tripal-addprefix"
+ - "traefik.http.routers.{{ genus_species }}-tripal.middlewares=sp-trailslash,sp-prefix,tripal-addprefix" # lg
+ - "traefik.http.services.{{ genus_species }}-tripal.loadbalancer.server.port=80"
+ restart_policy:
+ condition: on-failure
+ delay: 5s
+ max_attempts: 3
+ window: 120s
+
+ tripal-db:
+ image: quay.io/galaxy-genome-annotation/chado:1.31-jenkins26-pg9.5
+ environment:
+ - POSTGRES_PASSWORD=postgres
+ # The default chado image would try to install the schema on first run,
+ # we just want the tools to be available.
+ - INSTALL_CHADO_SCHEMA=0
+ volumes:
+ - ./docker_data/tripal_db/:/var/lib/postgresql/data/
+ networks:
+ - {{ genus_species }}
+
+ elasticsearch:
+ image: docker.elastic.co/elasticsearch/elasticsearch:6.6.1
+ #deploy:
+ #resources:
+ #limits:
+ #memory: 500M
+ volumes:
+ - ./docker_data/elastic_search_index/:/usr/share/elasticsearch/data/
+ environment:
+ bootstrap.memory_lock: "true"
+ xpack.security.enabled: "false"
+ xpack.monitoring.enabled: "false"
+ xpack.ml.enabled: "false"
+ xpack.graph.enabled: "false"
+ xpack.watcher.enabled: "false"
+ cluster.routing.allocation.disk.threshold_enabled: "false"
+ ES_JAVA_OPTS: "-Xms500m -Xmx500m"
+ TAKE_FILE_OWNERSHIP: "true"
+ networks:
+ - {{ genus_species }}
+
+ galaxy:
+ 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
+ - ./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/
+ - ./docker_data/apollo/:/apollo-data/
+ - ../galaxy_nginx.conf:/etc/nginx/uwsgi_params
+ environment:
+ NONUSE: nodejs,proftp,reports,condor
+ GALAXY_LOGGING: full
+ 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_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 }}"
+ ENABLE_FIX_PERMS: 0
+ PROXY_PREFIX: /sp/{{ genus_species }}/galaxy
+ GALAXY_TRIPAL_URL: http://tripal. {{ genus_species }}/tripal/
+ GALAXY_TRIPAL_PASSWORD: {{ tripal_password }} # See tripal config above
+ GALAXY_WEBAPOLLO_URL: http://one-of-the-swarm-node:8888/apollo/
+ GALAXY_WEBAPOLLO_USER: "{{ webapollo_user }}"
+ GALAXY_WEBAPOLLO_PASSWORD: "{{ webapollo_password }}" # See tripal config below
+ GALAXY_WEBAPOLLO_EXT_URL: /apollo/
+ GALAXY_CHADO_DBHOST: tripal-db.genus_species
+ GALAXY_CHADO_DBSCHEMA: chado
+ GALAXY_AUTO_UPDATE_DB: 1
+ GALAXY_AUTO_UPDATE_CONDA: 1
+ GALAXY_AUTO_UPDATE_TOOLS: "/galaxy-central/tools_1.yaml"
+ GALAXY_SHARED_DIR: ""
+ BLAT_ENABLED: 1
+ networks:
+ - traefikbig
+ - {{ genus_species }}
+ deploy:
+ labels:
+ - "traefik.http.routers.{{ genus_species }}-galaxy.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/galaxy`))"
+# - "traefik.http.routers.{{ genus_species }}-galaxy.tls=true"
+# - "traefik.http.routers.{{ genus_species }}-galaxy.entryPoints=webs"
+ - "traefik.http.routers.{{ genus_species }}-galaxy.entryPoints=web" #lg
+# - "traefik.http.routers.{{ genus_species }}-galaxy.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
+ - "traefik.http.routers.{{ genus_species }}-galaxy.middlewares=sp-app-trailslash,sp-app-prefix" #lg
+ - "traefik.http.services.{{ genus_species }}-galaxy.loadbalancer.server.port=80"
+ restart_policy:
+ condition: on-failure
+ delay: 5s
+ max_attempts: 3
+ window: 120s
+
+ jbrowse:
+ image: quay.io/galaxy-genome-annotation/jbrowse:v1.16.8
+ volumes:
+ - ./docker_data/galaxy/:/export/:ro
+ - ./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/:ro
+ networks:
+ - traefikbig
+ - {{ genus_species }}
+ deploy:
+ labels:
+ - "traefik.http.routers.{{ genus_species }}-jbrowse.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/jbrowse`))"
+# - "traefik.http.routers.{{ genus_species }}-jbrowse.tls=true"
+# - "traefik.http.routers.{{ genus_species }}-jbrowse.entryPoints=webs"
+ - "traefik.http.routers.{{ genus_species }}-jbrowse.entryPoints=web" # lg
+# - "traefik.http.routers.{{ genus_species }}-jbrowse.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
+ - "traefik.http.routers.{{ genus_species }}-jbrowse.middlewares=sp-app-trailslash,sp-app-prefix" #lg
+ - "traefik.http.services.{{ genus_species }}-jbrowse.loadbalancer.server.port=80"
+ restart_policy:
+ condition: on-failure
+ delay: 5s
+ max_attempts: 3
+ window: 120s
+
+ blast:
+ image: quay.io/abretaud/sf-blast:latest
+ depends_on:
+ - blast-db
+ environment:
+ DB_HOST: blast-db.{{ genus_species }}
+ UPLOAD_LIMIT: 20M
+ MEMORY_LIMIT: 128M
+ DB_NAME: 'postgres'
+ ADMIN_EMAIL: 'g.ga@sb-roscoff.fr' # email sender
+ ADMIN_NAME: 'gga' # email sender name
+ JOBS_METHOD: 'local' # Can be local (= no sge jobs, but run inside the container) or drmaa (= to submit to a cluster)
+ JOBS_WORK_DIR: '/tmp/blast_jobs/' # disk accessible both from compute nodes and mounted in this docker (at the same path)
+ CDD_DELTA_PATH: '/db/cdd_delta/current/flat/cdd_delta'
+ BLAST_TITLE: '{{ Genus }} {{ species }} blast server'
+ JOBS_SCHED_NAME: '{{ blast_gspecies }}' # job names
+ #PRE_CMD: '. /local/env/envblast-2.6.0.sh; . /local/env/envpython-3.7.1.sh;' # executed at the beginning of each job
+ #APACHE_RUN_USER: 'bipaaweb' # username known by sge
+ #APACHE_RUN_GROUP: 'bipaa' # group known by sge
+ BASE_URL_PATH: '/sp/{{ genus_species }}/blast/'
+ UID: 55914 # username known by sge (for drmaa mode only)
+ GID: 40259 # group known by sge (for drmaa mode only)
+ #JOBS_DRMAA_NATIVE: '-p web' # This line and following for slurm
+ #DRMAA_METHOD: 'slurm' # This line and following for slurm
+ volumes:
+ - ../blast-themes/abims/:/var/www/blast/app/Resources/:ro # You can theme the app
+ - /usr/local/genome2/:/usr/local/genome2/:ro # path for blast executables
+ - /db/:/db/:ro # for access to indexed blast databases
+ #- /data1/sge/:/usr/local/sge/:ro # an sge install
+ #- /xxxx/blast_jobs/:/xxxx/blast_jobs/ # (for drmaa mode only)
+ - ./blast/banks.yml:/var/www/blast/app/config/banks.yml:ro
+ - ./blast/links.yml:/etc/blast_links/links.yml:ro
+ #- /data1/slurm/slurm.conf:/etc/slurm-llnl/slurm.conf:ro # This line and following for slurm
+ #- /data1/slurm/gres.conf:/etc/slurm-llnl/gres.conf:ro
+ #- /data1/slurm/cgroup.conf:/etc/slurm-llnl/cgroup.conf:ro
+ #- /data1/slurm/slurmdbd.conf:/etc/slurm-llnl/slurmdbd.conf:ro
+ #- /data1/slurm/drmaa/:/etc/slurm-llnl/drmaa/:ro
+ #- /etc/munge/:/etc/munge/:ro
+ networks:
+ - traefikbig
+ - {{ genus_species }}
+ deploy:
+ labels:
+ - "traefik.http.routers.{{ genus_species }}-blast.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/blast`))"
+# - "traefik.http.routers.{{ genus_species }}-blast.tls=true"
+# - "traefik.http.routers.{{ genus_species }}-blast.entryPoints=webs"
+ - "traefik.http.routers.{{ genus_species }}-blast.entryPoints=web" # lg
+# - "traefik.http.routers.{{ genus_species }}-blast.middlewares=sp-big-req,sp-auth,sp-app-trailslash,sp-app-prefix"
+ - "traefik.http.routers.{{ genus_species }}-blast.middlewares=sp-big-req,sp-app-trailslash,sp-app-prefix" # lg
+ - "traefik.http.services.{{ genus_species }}-blast.loadbalancer.server.port=80"
+ restart_policy:
+ condition: on-failure
+ delay: 5s
+ max_attempts: 3
+ window: 120s
+
+ blast-db:
+# image: postgres:9.6-alpine
+ image: postgres:9.5
+ environment:
+ - POSTGRES_PASSWORD=postgres
+ - PGDATA=/var/lib/postgresql/data/
+ volumes:
+ - ./docker_data/blast_db/:/var/lib/postgresql/data/
+ networks:
+ - {{ genus_species }}
+
+# wiki:
+# image: quay.io/abretaud/mediawiki
+# environment:
+# MEDIAWIKI_SERVER: http://localhost
+# MEDIAWIKI_PROXY_PREFIX: /sp/{{ genus_species }}/wiki
+# MEDIAWIKI_SITENAME: {{ Genus }} {{ species }}
+# MEDIAWIKI_SECRET_KEY: XXXXXXXXXX
+# MEDIAWIKI_DB_HOST: wiki-db.{{genus_species }}
+# MEDIAWIKI_DB_PASSWORD: password
+# MEDIAWIKI_ADMIN_USER: abretaud # ldap user
+# depends_on:
+# - wiki-db
+# volumes:
+# - ./docker_data/wiki_uploads:/images
+# #- ../bipaa_wiki.png:/var/www/mediawiki/resources/assets/wiki.png:ro # To change the logo at the top left
+# networks:
+# - traefikbig
+# - {{ genus_species }}
+# deploy:
+# labels:
+# - "traefik.http.routers.{{ genus_species }}-blast.rule=(Host(`{{ hostname }}`) && PathPrefix(`/sp/{{ genus_species }}/blast`))"
+# - "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"
+# - "traefik.http.services.{{ genus_species }}-blast.loadbalancer.server.port=80"
+# restart_policy:
+# condition: on-failure
+# delay: 5s
+# max_attempts: 3
+# window: 120s
+
+# wiki-db:
+# image: postgres:9.6-alpine
+# volumes:
+# - ./docker_data/wiki_db/:/var/lib/postgresql/data/
+# networks:
+# - {{ genus_species }}
+
+networks:
+ traefikbig:
+ external: true
+ {{ genus_species }}:
+ driver: overlay
+ name: {{ genus_species }}
diff --git a/templates/traefik_compose_template.yml.j2 b/templates/traefik_compose_template.yml.j2
new file mode 100644
index 0000000..92aac2e
--- /dev/null
+++ b/templates/traefik_compose_template.yml.j2
@@ -0,0 +1,120 @@
+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={{ proxy_ip }}" # The ips of our upstream proxies: eci
+ - "--entryPoints.webs.address=:443"
+ - "--entryPoints.webs.forwardedHeaders.trustedIPs={{ proxy_ip }}" # The ips of our upstream proxies: eci
+ ports:
+ - {{ dashboard_port }}:8080 # added by lg to debug, for dashboard
+ - {{ http_port }}:80
+ - {{ https_port }}: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/utilities.py b/utilities.py
index 92ffce8..143c211 100644
--- a/utilities.py
+++ b/utilities.py
@@ -46,20 +46,15 @@ def parse_input(input_file):
parsed_sp_dict_list = []
- if str(input_file).endswith("yml") or str(input_file).endswith("yaml"):
- logging.debug("Input format used: YAML")
- else:
- logging.critical("Error, please input a YAML file")
- sys.exit()
try:
with open(input_file, 'r') as stream:
try:
yaml_dict = yaml.safe_load(stream)
for k, v in yaml_dict.items():
parsed_sp_dict_list.append(v)
- except yaml.YAMLError:
- logging.critical("YAML input file might be incorrect")
- sys.exit()
+ except yaml.YAMLError as err:
+ logging.critical("Input file is not in YAML format")
+ sys.exit(err)
except FileNotFoundError:
logging.critical("The specified input file doesn't exist (%s)" % input_file)
sys.exit()
diff --git a/workflows/Chado_load_Tripal_synchronize.ga b/workflows/Chado_load_Tripal_synchronize.ga
index c8ce7a4..f9e114c 100644
--- a/workflows/Chado_load_Tripal_synchronize.ga
+++ b/workflows/Chado_load_Tripal_synchronize.ga
@@ -16,7 +16,7 @@
"outputs": [],
"position": {
"left": 200,
- "top": 227
+ "top": 662.7333374023438
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
@@ -27,7 +27,7 @@
{
"label": null,
"output_name": "output",
- "uuid": "08f77326-1435-4fad-a610-e56f06a0ced5"
+ "uuid": "df303ec8-a34f-47ff-8e23-f6fd4f7a4a25"
}
]
},
@@ -43,7 +43,7 @@
"outputs": [],
"position": {
"left": 200,
- "top": 317
+ "top": 707.7333374023438
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
@@ -54,7 +54,7 @@
{
"label": null,
"output_name": "output",
- "uuid": "e8f16746-c91f-4147-b460-f1052650e699"
+ "uuid": "cae20d90-587c-4b3b-b3a4-5aedb8dde3bf"
}
]
},
@@ -70,7 +70,7 @@
"outputs": [],
"position": {
"left": 200,
- "top": 407
+ "top": 752.7333374023438
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
@@ -81,7 +81,7 @@
{
"label": null,
"output_name": "output",
- "uuid": "98ade546-95a4-477c-bd19-38d278849b98"
+ "uuid": "79cc48a0-de9b-45d1-8372-7dabded47796"
}
]
},
@@ -97,7 +97,7 @@
"outputs": [],
"position": {
"left": 200,
- "top": 497
+ "top": 797.7333374023438
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
@@ -108,7 +108,7 @@
{
"label": null,
"output_name": "output",
- "uuid": "41417aad-64e5-4480-9c36-842d0dda1c6d"
+ "uuid": "00f82694-ec6e-471c-90ab-66311651c023"
}
]
},
@@ -146,8 +146,8 @@
}
],
"position": {
- "left": 486,
- "top": 227
+ "left": 343,
+ "top": 662.7333374023438
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.3",
@@ -171,9 +171,62 @@
},
"5": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
"errors": null,
"id": 5,
+ "input_connections": {
+ "reference_genome|genome": {
+ "id": 0,
+ "output_name": "output"
+ },
+ "track_groups_0|data_tracks_0|data_format|annotation": {
+ "id": 1,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool JBrowse",
+ "name": "reference_genome"
+ }
+ ],
+ "label": null,
+ "name": "JBrowse",
+ "outputs": [
+ {
+ "name": "output",
+ "type": "html"
+ }
+ ],
+ "position": {
+ "left": 343,
+ "top": 748.7333374023438
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+ "tool_shed_repository": {
+ "changeset_revision": "8774b28235bb",
+ "name": "jbrowse",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_label\": \"View transcript report\", \"menu_title\": \"Transcript {id}\", \"menu_url\": {\"__class__\": \"RuntimeValue\"}, \"menu_icon\": \"dijitIconBookmark\"}]}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "1.16.10+galaxy0",
+ "type": "tool",
+ "uuid": "00657cb2-12f9-4f93-98da-04feac9e1388",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "6cbfa232-911e-49b9-96ad-fa9ed236f806"
+ }
+ ]
+ },
+ "6": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
+ "errors": null,
+ "id": 6,
"input_connections": {
"fasta": {
"id": 2,
@@ -193,21 +246,9 @@
"description": "runtime parameter for tool Chado load gff",
"name": "analysis_id"
},
- {
- "description": "runtime parameter for tool Chado load gff",
- "name": "fasta"
- },
- {
- "description": "runtime parameter for tool Chado load gff",
- "name": "gff"
- },
{
"description": "runtime parameter for tool Chado load gff",
"name": "organism"
- },
- {
- "description": "runtime parameter for tool Chado load gff",
- "name": "wait_for"
}
],
"label": null,
@@ -219,8 +260,8 @@
}
],
"position": {
- "left": 772,
- "top": 227
+ "left": 486,
+ "top": 743.2333374023438
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
@@ -230,7 +271,7 @@
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"add_only\": \"false\", \"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"gff\": {\"__class__\": \"RuntimeValue\"}, \"landmark_type\": \"contig\", \"no_seq_compute\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"prot_naming\": {\"method\": \"regex\", \"__current_case__\": 1, \"re_protein_capture\": \"^mRNA(\\\\..+)$\", \"re_protein\": \"protein\\\\1\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"add_only\": \"false\", \"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gff\": {\"__class__\": \"ConnectedValue\"}, \"landmark_type\": \"contig\", \"no_seq_compute\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"prot_naming\": {\"method\": \"regex\", \"__current_case__\": 1, \"re_protein_capture\": \"^mRNA(\\\\..+)$\", \"re_protein\": \"protein\\\\1\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.3.3",
"type": "tool",
"uuid": "b100a055-0dab-4f2f-8c46-573713ed3fff",
@@ -242,14 +283,58 @@
}
]
},
- "6": {
+ "7": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
+ "errors": null,
+ "id": 7,
+ "input_connections": {
+ "organisms_0|jbrowse": {
+ "id": 5,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "Add organisms to JBrowse container",
+ "outputs": [
+ {
+ "name": "output",
+ "type": "html"
+ }
+ ],
+ "position": {
+ "left": 486,
+ "top": 662.7333374023438
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
+ "tool_shed_repository": {
+ "changeset_revision": "11033bdad2ca",
+ "name": "jbrowse_to_container",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"organisms\": [{\"__index__\": 0, \"jbrowse\": {\"__class__\": \"RuntimeValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"advanced\": {\"unique_id\": {\"__class__\": \"RuntimeValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "0.5.1",
+ "type": "tool",
+ "uuid": "7b7cca87-4000-45de-93a5-bd22cd661d0a",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "8c23d473-4ffa-4a66-b071-aeecc105a529"
+ }
+ ]
+ },
+ "8": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_organism_sync/organism_sync/3.2.1.0",
"errors": null,
- "id": 6,
+ "id": 8,
"input_connections": {
"wait_for": {
- "id": 5,
+ "id": 6,
"output_name": "results"
}
},
@@ -268,8 +353,8 @@
}
],
"position": {
- "left": 1058,
- "top": 227
+ "left": 629,
+ "top": 662.7333374023438
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_organism_sync/organism_sync/3.2.1.0",
@@ -291,14 +376,14 @@
}
]
},
- "7": {
+ "9": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"errors": null,
- "id": 7,
+ "id": 9,
"input_connections": {
"wait_for": {
- "id": 6,
+ "id": 8,
"output_name": "results"
}
},
@@ -317,8 +402,8 @@
}
],
"position": {
- "left": 1344,
- "top": 227
+ "left": 772,
+ "top": 662.7333374023438
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
@@ -340,14 +425,14 @@
}
]
},
- "8": {
+ "10": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"errors": null,
- "id": 8,
+ "id": 10,
"input_connections": {
"wait_for": {
- "id": 7,
+ "id": 9,
"output_name": "results"
}
},
@@ -366,8 +451,8 @@
}
],
"position": {
- "left": 1630,
- "top": 227
+ "left": 915,
+ "top": 662.7333374023438
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
@@ -389,14 +474,14 @@
}
]
},
- "9": {
+ "11": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
"errors": null,
- "id": 9,
+ "id": 11,
"input_connections": {
"wait_for": {
- "id": 8,
+ "id": 10,
"output_name": "results"
}
},
@@ -415,8 +500,8 @@
}
],
"position": {
- "left": 1916,
- "top": 227
+ "left": 1058,
+ "top": 662.7333374023438
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
@@ -440,6 +525,6 @@
}
},
"tags": [],
- "uuid": "00c4d6e1-f470-4b31-9cc1-402aa9b598e2",
- "version": 1
+ "uuid": "69699b44-94c8-4cc7-977e-74f266e58fdf",
+ "version": 3
}
\ No newline at end of file
diff --git a/workflows/Chado_load_Tripal_synchronize.ga.bak b/workflows/Chado_load_Tripal_synchronize.ga.bak
index a194b03..c8ce7a4 100644
--- a/workflows/Chado_load_Tripal_synchronize.ga.bak
+++ b/workflows/Chado_load_Tripal_synchronize.ga.bak
@@ -16,14 +16,20 @@
"outputs": [],
"position": {
"left": 200,
- "top": 200
+ "top": 227
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "89e7487e-004d-4db1-b5eb-1676b98aebde",
- "workflow_outputs": []
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "08f77326-1435-4fad-a610-e56f06a0ced5"
+ }
+ ]
},
"1": {
"annotation": "",
@@ -37,14 +43,20 @@
"outputs": [],
"position": {
"left": 200,
- "top": 290
+ "top": 317
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "1d25f54c-7575-4c8d-be55-73dd7e58613f",
- "workflow_outputs": []
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "e8f16746-c91f-4147-b460-f1052650e699"
+ }
+ ]
},
"2": {
"annotation": "",
@@ -58,14 +70,20 @@
"outputs": [],
"position": {
"left": 200,
- "top": 380
+ "top": 407
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "6c1a20fa-828a-404c-b107-76fb8ddf3954",
- "workflow_outputs": []
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "98ade546-95a4-477c-bd19-38d278849b98"
+ }
+ ]
},
"3": {
"annotation": "",
@@ -79,38 +97,44 @@
"outputs": [],
"position": {
"left": 200,
- "top": 470
+ "top": 497
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "74f22d9b-e764-45e4-b0eb-579c9b647ea0",
- "workflow_outputs": []
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "41417aad-64e5-4480-9c36-842d0dda1c6d"
+ }
+ ]
},
"4": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.3",
"errors": null,
"id": 4,
"input_connections": {
"fasta": {
- "id": 3,
+ "id": 0,
"output_name": "output"
},
"wait_for": {
- "id": 3,
+ "id": 0,
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load fasta",
- "name": "fasta"
+ "name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load fasta",
- "name": "wait_for"
+ "name": "organism"
}
],
"label": null,
@@ -123,31 +147,31 @@
],
"position": {
"left": 486,
- "top": 200
+ "top": 227
},
"post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.3",
"tool_shed_repository": {
- "changeset_revision": "ba4d07fbaf47",
+ "changeset_revision": "a7ab30ded37d",
"name": "chado_feature_load_fasta",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"analysis_id\": \"1\", \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism\": \"2\", \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.3.4+galaxy0",
+ "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"match_on_name\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.3",
"type": "tool",
- "uuid": "ed72bf37-aa81-4b25-8ab4-dccb54bc68d9",
+ "uuid": "f7a44182-3620-4a19-9e67-94fe584d4206",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
- "uuid": "c617e0d3-a44c-4fb1-b831-22a487a6be6a"
+ "uuid": "24ed7255-b4a6-4000-b82b-c18d81822262"
}
]
},
"5": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
"errors": null,
"id": 5,
"input_connections": {
@@ -165,6 +189,10 @@
}
},
"inputs": [
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "analysis_id"
+ },
{
"description": "runtime parameter for tool Chado load gff",
"name": "fasta"
@@ -173,6 +201,10 @@
"description": "runtime parameter for tool Chado load gff",
"name": "gff"
},
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "organism"
+ },
{
"description": "runtime parameter for tool Chado load gff",
"name": "wait_for"
@@ -188,25 +220,25 @@
],
"position": {
"left": 772,
- "top": 200
+ "top": 227
},
"post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
"tool_shed_repository": {
- "changeset_revision": "e9a6d7568817",
+ "changeset_revision": "6fdfbf0caa8c",
"name": "chado_feature_load_gff",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"add_only\": \"false\", \"analysis_id\": \"1\", \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"gff\": {\"__class__\": \"RuntimeValue\"}, \"landmark_type\": \"\", \"no_seq_compute\": \"false\", \"organism\": \"2\", \"prot_naming\": {\"method\": \"auto\", \"__current_case__\": 0}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.3.4+galaxy0",
+ "tool_state": "{\"add_only\": \"false\", \"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"gff\": {\"__class__\": \"RuntimeValue\"}, \"landmark_type\": \"contig\", \"no_seq_compute\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"prot_naming\": {\"method\": \"regex\", \"__current_case__\": 1, \"re_protein_capture\": \"^mRNA(\\\\..+)$\", \"re_protein\": \"protein\\\\1\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.3",
"type": "tool",
- "uuid": "0b5746d7-952d-4aff-b688-4666c13cab8a",
+ "uuid": "b100a055-0dab-4f2f-8c46-573713ed3fff",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
- "uuid": "5da80c86-c510-425a-b8e1-475ab26436f3"
+ "uuid": "d0ce6d85-fb8b-4509-9784-a8ded1aeae05"
}
]
},
@@ -237,15 +269,9 @@
],
"position": {
"left": 1058,
- "top": 200
- },
- "post_job_actions": {
- "HideDatasetActionresults": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "results"
- }
+ "top": 227
},
+ "post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_organism_sync/organism_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "afd5d92745fb",
@@ -256,8 +282,14 @@
"tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "05314408-41fa-4a2f-8aae-3988e2d899f6",
- "workflow_outputs": []
+ "uuid": "040183a5-1aba-4bf6-9669-c6e93cfff3ea",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "f1f2dc7a-37e2-4bd3-b997-8f1e3eed11aa"
+ }
+ ]
},
"7": {
"annotation": "",
@@ -286,15 +318,9 @@
],
"position": {
"left": 1344,
- "top": 200
- },
- "post_job_actions": {
- "HideDatasetActionresults": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "results"
- }
+ "top": 227
},
+ "post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "f487ff676088",
@@ -305,8 +331,14 @@
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "44c7cc7c-0848-47a7-872c-351f057803c1",
- "workflow_outputs": []
+ "uuid": "6096e174-c85d-4e50-916f-a396d58a909b",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "a309f4e4-3402-4eb5-8b70-1acfa1f26bb4"
+ }
+ ]
},
"8": {
"annotation": "",
@@ -335,15 +367,9 @@
],
"position": {
"left": 1630,
- "top": 200
- },
- "post_job_actions": {
- "HideDatasetActionresults": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "results"
- }
+ "top": 227
},
+ "post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "f487ff676088",
@@ -354,8 +380,14 @@
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "8ce8c990-39ce-4725-892b-4216a75f487d",
- "workflow_outputs": []
+ "uuid": "d6072bb6-036d-4fbf-893c-d25f139a05ac",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "ff817e04-d0ce-461f-a97a-843e36a25aca"
+ }
+ ]
},
"9": {
"annotation": "",
@@ -384,15 +416,9 @@
],
"position": {
"left": 1916,
- "top": 200
- },
- "post_job_actions": {
- "HideDatasetActionresults": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "results"
- }
+ "top": 227
},
+ "post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "64e36c3f0dd6",
@@ -400,14 +426,20 @@
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"repeat_ids\": [], \"repeat_types\": [{\"__index__\": 0, \"types\": \"mRNA\"}, {\"__index__\": 1, \"types\": \"popylpeptide\"}], \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"repeat_ids\": [], \"repeat_types\": [{\"__index__\": 0, \"types\": \"mRNA\"}, {\"__index__\": 1, \"types\": \"polypeptide\"}], \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "04600903-dd16-4db1-b562-552aeb003e6c",
- "workflow_outputs": []
+ "uuid": "9d39d394-7375-4187-86f3-6dc676c9ca30",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "5047a899-60e2-4acc-a95f-4f60f83c32ae"
+ }
+ ]
}
},
"tags": [],
- "uuid": "4c66363e-ff14-4c79-8edf-9ab05cafa33d",
- "version": 2
+ "uuid": "00c4d6e1-f470-4b31-9cc1-402aa9b598e2",
+ "version": 1
}
\ No newline at end of file
diff --git a/workflows/Jbrowse.ga b/workflows/Jbrowse.ga
index 5c4ac95..cbbc200 100644
--- a/workflows/Jbrowse.ga
+++ b/workflows/Jbrowse.ga
@@ -27,7 +27,7 @@
{
"label": null,
"output_name": "output",
- "uuid": "6015fbdd-dc71-4fb8-916d-2241f37693c4"
+ "uuid": "6fddadc5-3420-4747-920f-7816c926f16b"
}
]
},
@@ -54,7 +54,7 @@
{
"label": null,
"output_name": "output",
- "uuid": "c0667455-6271-4d1f-9388-75ec65762bb4"
+ "uuid": "d29ec40e-71fb-4960-94d5-af4666ad1c1d"
}
]
},
@@ -99,7 +99,7 @@
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"transcript\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_label\": \"View transcript report\", \"menu_title\": \"Transcript {id}\", \"menu_url\": {\"__class__\": \"RuntimeValue\"}, \"menu_icon\": \"dijitIconBookmark\"}]}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"test\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"test\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"mRNA\"}}, \"jbstyle\": {\"style_classname\": \"transcript\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_label\": \"View transcript report\", \"menu_title\": \"Transcript {id}\", \"menu_url\": {\"__class__\": \"RuntimeValue\"}, \"menu_icon\": \"dijitIconBookmark\"}]}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.16.10+galaxy0",
"type": "tool",
"uuid": "ba7d15fd-8ffd-407d-9a45-47cd4be68bd2",
@@ -143,7 +143,7 @@
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"organisms\": [{\"__index__\": 0, \"jbrowse\": {\"__class__\": \"RuntimeValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"advanced\": {\"unique_id\": \"\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"organisms\": [{\"__index__\": 0, \"jbrowse\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"advanced\": {\"unique_id\": {\"__class__\": \"RuntimeValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.5.1",
"type": "tool",
"uuid": "1cf25ca3-2287-4b82-9e93-b8828eed70a2",
@@ -157,6 +157,6 @@
}
},
"tags": [],
- "uuid": "e12dd4c9-0012-4d14-9cd2-8313a99c71cc",
- "version": 1
+ "uuid": "7745ddc9-190a-436d-9bd3-2318e9d568a8",
+ "version": 0
}
\ No newline at end of file
diff --git a/workflows/Jbrowse.ga.bak b/workflows/Jbrowse.ga.bak
new file mode 100644
index 0000000..7e2c31e
--- /dev/null
+++ b/workflows/Jbrowse.ga.bak
@@ -0,0 +1,157 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "Jbrowse",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 200
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "751caac1-d015-4d77-8a68-2c3debae0caf",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "6955cc2b-d4d6-484b-8a89-6e4c5dcca879"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
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GitLab