From 0a5b7a63405e0576adc595f92b58e5358821e3dc Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 19 Jan 2021 17:09:00 +0100
Subject: [PATCH] run_workflow changes (functional again), some optimisation in
gga_init, gga_load and run_workflow, more validation steps in gga_init
---
config => examples/config | 2 +-
examples/config_demo.yaml | 21 ++
.../{yml_example_input.yml => example.yml} | 0
examples/{demo.yaml => input_demo.yaml} | 0
gga_init.py | 46 +--
gga_load_data.py | 5 +-
run_workflow_phaeoexplorer.py | 74 +++--
..._users.yml => authelia_users_template.yml} | 0
templates/compose_template.bk.yml | 302 ------------------
...late.yml => gspecies_compose_template.yml} | 0
..._nginx.conf => nginx_apollo_template.conf} | 0
...ginx.conf => nginx_download_template.conf} | 0
...aefik.yml => traefik_compose_template.yml} | 0
utils/docker_compose_generator.py | 73 +++++
utils/metadata_generator.py | 36 +++
workflows/phaeoexplorer_base_workflow.ga | 1 -
workflows/phaeoexplorer_jbrowse_workflow.ga | 1 -
17 files changed, 203 insertions(+), 358 deletions(-)
rename config => examples/config (96%)
create mode 100644 examples/config_demo.yaml
rename examples/{yml_example_input.yml => example.yml} (100%)
rename examples/{demo.yaml => input_demo.yaml} (100%)
rename templates/{authelia_users.yml => authelia_users_template.yml} (100%)
delete mode 100644 templates/compose_template.bk.yml
rename templates/{compose_template.yml => gspecies_compose_template.yml} (100%)
rename templates/{apollo_nginx.conf => nginx_apollo_template.conf} (100%)
rename templates/{download_nginx.conf => nginx_download_template.conf} (100%)
rename templates/{traefik.yml => traefik_compose_template.yml} (100%)
create mode 100755 utils/docker_compose_generator.py
create mode 100755 utils/metadata_generator.py
delete mode 100644 workflows/phaeoexplorer_base_workflow.ga
delete mode 100644 workflows/phaeoexplorer_jbrowse_workflow.ga
diff --git a/config b/examples/config
similarity index 96%
rename from config
rename to examples/config
index 0501bd7..527f310 100644
--- a/config
+++ b/examples/config
@@ -3,7 +3,7 @@
# "all" section contains variables used by several services at once or the paths to import sensible files that cannot be procedurally generated/formatted using the scripts
all:
- custom_host: your_host # The hosting machine name
+ custom_host: localhost # The hosting machine name
custom_authelia_config_path: /path/to/your/authelia/config # The path to the authelia config yml to use, an example is available in the "examples" folder at the repo root
# "galaxy" section contains variables used to set up the galaxy service
galaxy:
diff --git a/examples/config_demo.yaml b/examples/config_demo.yaml
new file mode 100644
index 0000000..527f310
--- /dev/null
+++ b/examples/config_demo.yaml
@@ -0,0 +1,21 @@
+# This is the configuration file used by the gga_init.py, gga_load_data.py and run_workflow.py scripts
+# It contains (sensible) variables to set up different docker services
+
+# "all" section contains variables used by several services at once or the paths to import sensible files that cannot be procedurally generated/formatted using the scripts
+all:
+ custom_host: localhost # The hosting machine name
+ custom_authelia_config_path: /path/to/your/authelia/config # The path to the authelia config yml to use, an example is available in the "examples" folder at the repo root
+# "galaxy" section contains variables used to set up the galaxy service
+galaxy:
+ custom_galaxy_default_admin_email: admin@galaxy.org # The default admin email (used to connect to the instance)
+ custom_galaxy_defaut_admin_user: admin # The default admin user
+ custom_galaxy_default_admin_password: password # The default admin password (used to connect to the instance)
+ custom_galaxy_config_master_api_key: master # The master API key (not in use at the moment so you can skip this)
+ custom_galaxy_tripal_password: galaxy_tripal_password # Same as custom_tripal_admin_password (connection to db relies on this)
+ custom_galaxy_web_apollo_user: admin_apollo@galaxy.org # Apollo user
+ custom_galaxy_web_apollo_password: galaxy_apollo_password # Apollo password tied to the user above
+tripal:
+ custom_tripal_admin_password: galaxy_tripal_password # Same as custom_galay_tripal_password (connection to db relies on this)
+ custom_banner: /path/to/banner # Custom banner, TODO: defaults to a generic banner
+ custom_theme: "abims_gga" # Use this to use another theme
+ custom_theme_git_clone: "http://gitlab.sb-roscoff.fr/abims/e-infra/tripal_gga.git" # Use this to install another theme than the default one
\ No newline at end of file
diff --git a/examples/yml_example_input.yml b/examples/example.yml
similarity index 100%
rename from examples/yml_example_input.yml
rename to examples/example.yml
diff --git a/examples/demo.yaml b/examples/input_demo.yaml
similarity index 100%
rename from examples/demo.yaml
rename to examples/input_demo.yaml
diff --git a/gga_init.py b/gga_init.py
index 9fd72ae..393e5cc 100644
--- a/gga_init.py
+++ b/gga_init.py
@@ -49,23 +49,27 @@ class DeploySpeciesStack(speciesData.SpeciesData):
logging.info("Updating directory tree for %s" % self.full_name)
try:
os.chdir(self.species_dir)
- working_dir = os.getcwd()
except OSError:
logging.critical("Cannot access " + self.species_dir + ", run with higher privileges")
sys.exit()
# Copy the custom banner to the species dir (banner used in tripal pages)
- # To change the banner, replace the "banner.png" file in the "misc" folder of the archive
- if not os.path.isfile("%s/banner.png" % self.species_dir):
- shutil.copy("%s/misc/banner.png" % self.script_dir, "%s/banner.png" % self.species_dir)
+ if not self.config["custom_banner"] or self.config["custom_banner"] == "/path/to/banner" or self.config["custom_banner"] == "":
+ try:
+ 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("Custom banner (%s), skipping" % self.config["custom_banner"])
+
+ # Copy nginx conf
try:
os.mkdir("./nginx/")
os.mkdir("./nginx/conf")
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 FileExistsError:
- logging.debug("NginX conf exists")
+ logging.debug("Nginx conf already exists, skipping")
organism_annotation_dir, organism_genome_dir = None, None
@@ -116,6 +120,8 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Return to main_dir
os.chdir(self.main_dir)
+ logging.info("Directory tree generated for %s" % self.full_name)
+
def make_compose_files(self):
"""
@@ -132,10 +138,10 @@ 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/compose_template.yml"
- traefik_template_path = self.script_dir + "/templates/traefik.yml"
+ stack_template_path = self.script_dir + "/templates/gspecies_compose_template.yml"
+ 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.yml"
+ authelia_users_path = self.script_dir + "/templates/authelia_users_template.yml"
# Set the genus_species_strain_sex var, used
genus_species_strain_sex = "{0}_{1}".format(self.genus.lower(), self.species)
@@ -172,26 +178,21 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Create mounts for the current docker-compose
self.create_mounts(working_dir=self.species_dir)
- # TODO: obsolete?
- # Call create_mounts.py (replace subprocess.DEVNULL by subprocess.PIPE to get script stdout and stderr back)
- # subprocess.call(["python3", self.script_dir + "/create_mounts.py"], cwd=self.species_dir,
- # stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) # Create mounts for the containers
-
- # Store the traefik directory path to be able to create volumes for the traefik containers
- traefik_dir = None
try:
os.chdir(os.path.abspath(self.main_dir))
os.mkdir("./traefik")
os.mkdir("./traefik/authelia")
if self.config["custom_authelia_config_path"]:
- print("Authelia configuration found in the config file, placing it in ./traefik/authelia/")
-
- # if not os.path.isfile("../traefik/authelia/configuration.yml"): # TODO: obsolete?
- # shutil.copy(authelia_config_path, "../traefik/authelia/configuration.yml") # change variables by hand and adds the path of your authelia configuration in the config file
+ if os.path.isfile(os.path.abspath(self.config["custom_authelia_config_path"])):
+ try:
+ shutil.copy(os.path.abspath(self.config["custom_authelia_config_path"]), "./traefik/authelia")
+ except FileNotFoundError:
+ logging.critical("Cannot copy custom Authelia config file (%s)" % self.config["custom_authelia_config_path"])
+ sys.exit()
+ else:
+ logging.critical("Custom Authelia config file not found (%s)" % self.config["custom_authelia_config_path"])
if not os.path.isfile("./traefik/authelia/users.yml"):
shutil.copy(authelia_users_path, "./traefik/authelia/users.yml")
- # subprocess.call(["python3", self.script_dir + "/create_mounts.py"], cwd=self.species_dir,
- # stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) # Create mounts for the containers # TODO: obsolete?
except FileExistsError:
logging.debug("Traefik directory already exists: %s" % os.path.abspath("../traefik"))
try:
@@ -206,7 +207,6 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Create the mounts for the traefik+authelia containers
self.create_mounts(working_dir=traefik_dir)
- # subprocess.call(["python3", self.script_dir + "/create_mounts.py"], cwd=self.species_dir) # TODO: obsolete?
os.chdir(self.main_dir)
@@ -384,7 +384,7 @@ if __name__ == "__main__":
logging.info("Stack deployed for %s" % deploy_stack_for_current_organism.full_name)
- # TODO: IF GENUS°1 == GENUS°2 AND SP°1 == SP°2 --> SKIP INIT, CONTINUE TO NEXT ITEM IN INPUT
+ # TODO: IF GENUS°1 == GENUS°2 AND SP°1 == SP°2 --> SKIP INIT, CONTINUE TO NEXT ITEM IN INPUT (DEPLOY AT THE END)
# TODO: RELOAD TRAEFIK OUTSIDE LOOP
logging.info("All stacks deployed for organisms in input file %s" % args.input)
diff --git a/gga_load_data.py b/gga_load_data.py
index cff2747..ea60431 100644
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -628,6 +628,7 @@ if __name__ == "__main__":
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
+ logging.getLogger("urllib3").setLevel(logging.WARNING)
# Parsing the config file if provided, using the default config otherwise
if not args.config:
@@ -703,12 +704,10 @@ if __name__ == "__main__":
logging.info("Successfully set up library in galaxy for %s" % load_data_for_current_species.full_name)
# # Set or get the history for the current organism
- # load_data_for_current_species.set_get_history()
+ load_data_for_current_species.set_get_history()
# Remove H. sapiens from database if here TODO: set a dedicated history for removing H. sapiens (instead of doing it into a species history)
- # logging.info("Removing H. sapiens from Chado database for %s" % load_data_for_current_species.full_name)
load_data_for_current_species.remove_homo_sapiens_from_db()
- # logging.info("Successfully removed H. sapiens from Chado database for %s" % load_data_for_current_species.full_name)
# logging.info("Importing datasets into history for %s" % load_data_for_current_species.full_name)
# load_data_for_current_species.import_datasets_into_history()
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 35e645f..5485c6c 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -102,7 +102,9 @@ class RunWorkflow(speciesData.SpeciesData):
# Find genome folder datasets
genome_fasta_ldda_id = genome_folder_content["folder_contents"][0]["ldda_id"]
-
+
+ annotation_gff_ldda_id, annotation_proteins_ldda_id, annotation_transcripts_ldda_id = None, None, None
+
# Several dicts in the annotation folder content (one dict = one file)
for k, v in annotation_folder_content.items():
if k == "folder_contents":
@@ -122,13 +124,11 @@ 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"])
@@ -234,7 +234,7 @@ class RunWorkflow(speciesData.SpeciesData):
:return:
"""
- logging.info("importing workflow: " + str(workflow_path))
+ logging.info("Importing workflow: " + str(workflow_path))
workflow_name = "demo" # for workflow demo
workflow_ga_file = workflow_path
@@ -271,12 +271,12 @@ class RunWorkflow(speciesData.SpeciesData):
workflow_dict = json.load(ga_in_file)
self.instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)
- self.workflow_name = workflow_name
- workflow_attributes = self.instance.workflows.get_workflows(name=self.workflow_name)
+ workflow_attributes = self.instance.workflows.get_workflows(name=workflow_name)
workflow_id = workflow_attributes[0]["id"]
show_workflow = self.instance.workflows.show_workflow(workflow_id=workflow_id)
logging.debug("Workflow ID: " + workflow_id)
+ logging.info("Running workflow: %s" % workflow_name)
self.instance.workflows.invoke_workflow(workflow_id=workflow_id,
history_id=self.history_id,
params=workflow_parameters,
@@ -287,7 +287,7 @@ class RunWorkflow(speciesData.SpeciesData):
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
+ Find datasets in a library, get their ID and import them into the current history if they are not already
:return:
"""
@@ -356,6 +356,8 @@ class RunWorkflow(speciesData.SpeciesData):
Retrieve current organism ID and OGS and genome chado analyses IDs (needed to run some tools as Tripal/Chado
doesn't accept organism/analyses names as valid inputs
+ WARNING: It is mandatory to call this function before invoking a workflow
+
:return:
"""
# Get the ID for the current organism in chado
@@ -434,6 +436,8 @@ if __name__ == "__main__":
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
+ logging.getLogger("urllib3").setLevel(logging.INFO)
+ logging.getLogger("bioblend").setLevel(logging.INFO)
# Parsing the config file if provided, using the default config otherwise
if not args.config:
@@ -489,13 +493,14 @@ if __name__ == "__main__":
# Prepare the instance+history for the current organism (add organism and analyses in Chado) --> add argument?
# (althought there is no risk as chado refuses to duplicate an analysis/organism)
- run_workflow_for_current_organism.prepare_history()
+ # 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 (needs to be done in gga_load_data??)
- run_workflow_for_current_organism.import_datasets_into_history()
+ # run_workflow_for_current_organism.import_datasets_into_history()
workflow_parameters = dict()
@@ -506,21 +511,18 @@ if __name__ == "__main__":
# DEMO WORKFLOW
PARAM_LOAD_FASTA_IN_HISTORY = "0"
PARAM_LOAD_FASTA_IN_CHADO = "1"
- # PARAM_SYNC_ORGANISM_INTO_TRIPAL = "2"
- # PARAM_SYNC_GENOME_ANALYSIS_INTO_TRIPAL = "3"
- # PARAM_SYNC_FEATURES_INTO_TRIPAL = "4"
- # Mapping parameters
+ # Workflow inputs
workflow_parameters[PARAM_LOAD_FASTA_IN_HISTORY] = {}
workflow_parameters[PARAM_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"}
- # workflow_parameters[PARAM_SYNC_ORGANISM_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
- # workflow_parameters[PARAM_SYNC_GENOME_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
- # workflow_parameters[PARAM_SYNC_FEATURES_INTO_TRIPAL] = {"organism_id": 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" to prevent appending to the fasta file in chado
+ # It is safer to never update it and completely delete and restart the galaxy+tripal services instead (no workaround at the moment)
run_workflow_for_current_organism.datamap = dict()
- run_workflow_for_current_organism.datamap[PARAM_LOAD_FASTA_IN_HISTORY] = {"src": "hda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
+
+ # Datamap for input datasets - dataset source (type): ldda (LibraryDatasetDatasetAssociation)
+ run_workflow_for_current_organism.datamap[PARAM_LOAD_FASTA_IN_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
"""COMMENTED FOR THE DEMO"""
@@ -548,13 +550,31 @@ if __name__ == "__main__":
# workflow_parameters[PARAM_SYNC_OGS_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.genome_analysis_id}
# workflow_parameters[PARAM_SYNC_FEATURES_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
- # # Loading files into history works a bit different than the others as it's not a GMOD tool but a standard Galaxy tool
- # # It requires this additional "datamap" (conveniently named "datamap" here), requiring the source type of the file and its corresponding ID (unique)
+ # Loading files into history works a bit different than the others as it's not a GMOD tool but a standard Galaxy tool
+ # It requires this additional "datamap" (conveniently named "datamap" here), requiring the source type of the file and its corresponding ID (unique)
+ # The comments taken from the bioblend docs:
+ # """
+ # A mapping of workflow inputs to datasets and dataset collections.
+ # The datasets source can be a LibraryDatasetDatasetAssociation (``ldda``),
+ # LibraryDataset (``ld``), HistoryDatasetAssociation (``hda``), or
+ # HistoryDatasetCollectionAssociation (``hdca``).
+ #
+ # The map must be in the following format:
+ # ``{'<input_index>': {'id': <encoded dataset ID>, 'src': '[ldda, ld, hda, hdca]'}}``
+ # (e.g. ``{'2': {'id': '29beef4fadeed09f', 'src': 'hda'}}``)
+ #
+ # This map may also be indexed by the UUIDs of the workflow steps,
+ # as indicated by the ``uuid`` property of steps returned from the
+ # Galaxy API. Alternatively workflow steps may be addressed by
+ # the label that can be set in the workflow editor. If using
+ # uuid or label you need to also set the ``inputs_by`` parameter
+ # to ``step_uuid`` or ``name``.
+ # """
# run_workflow_for_current_organism.datamap = dict()
- # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE1_INTO_HISTORY] = {"src": "hda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
- # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE2_INTO_HISTORY] = {"src": "hda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
- # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE3_INTO_HISTORY] = {"src": "hda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
- # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE4_INTO_HISTORY] = {"src": "hda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
+ # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE1_INTO_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
+ # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE2_INTO_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
+ # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE3_INTO_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
+ # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE4_INTO_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
# Run the workflow with the parameters set above
run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
diff --git a/templates/authelia_users.yml b/templates/authelia_users_template.yml
similarity index 100%
rename from templates/authelia_users.yml
rename to templates/authelia_users_template.yml
diff --git a/templates/compose_template.bk.yml b/templates/compose_template.bk.yml
deleted file mode 100644
index 103757f..0000000
--- a/templates/compose_template.bk.yml
+++ /dev/null
@@ -1,302 +0,0 @@
-# ./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(`scratchgmodv1`) && 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
- #- /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_strain_sex
- ENABLE_APOLLO: 0
- ENABLE_BLAST: 1
- ENABLE_DOWNLOAD: 1
- ENABLE_WIKI: 0
- ENABLE_GO: 0
- ENABLE_ORTHOLOGY: 0
- ENABLE_ORTHOLOGY_LINKS: 0
- THEME: "abims" # Use this to use another theme
- THEME_GIT_CLONE: "http://gga:BuH1_aG5@gitlab.sb-roscoff.fr/abims/e-infra/tripal_abims" # Use this to install another theme
- ADMIN_PASSWORD: 23fN,Ajt # You need to define it and update it in galaxy config below --> change in prod (set a password in script init?)
- networks:
- - traefikbig
- - genus_species
- deploy:
- labels:
- - "traefik.http.routers.genus_species-tripal.rule=(Host(`scratchgmodv1`) && 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/
- - ./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: "gga@sb-roscoff.fr"
- GALAXY_DEFAULT_ADMIN_USER: "gga"
- GALAXY_DEFAULT_ADMIN_PASSWORD: "password"
- GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org, gga@sb-roscoff.fr, lgueguen@sb-roscoff.fr, alebars@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: "master"
- ENABLE_FIX_PERMS: 0
- PROXY_PREFIX: /sp/genus_species/galaxy
- GALAXY_TRIPAL_URL: http://tripal.genus_species/tripal/
- GALAXY_TRIPAL_PASSWORD: 23fN,Ajt # See tripal config above
- GALAXY_WEBAPOLLO_URL: http://one-of-the-swarm-node:8888/apollo/
- GALAXY_WEBAPOLLO_USER: "admin_apollo@sb-roscoff.fr"
- GALAXY_WEBAPOLLO_PASSWORD: "Q65:dA,t" # 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(`scratchgmodv1`) && 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(`scratchgmodv1`) && 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(`scratchgmodv1`) && 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(`localhost`) && 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/compose_template.yml b/templates/gspecies_compose_template.yml
similarity index 100%
rename from templates/compose_template.yml
rename to templates/gspecies_compose_template.yml
diff --git a/templates/apollo_nginx.conf b/templates/nginx_apollo_template.conf
similarity index 100%
rename from templates/apollo_nginx.conf
rename to templates/nginx_apollo_template.conf
diff --git a/templates/download_nginx.conf b/templates/nginx_download_template.conf
similarity index 100%
rename from templates/download_nginx.conf
rename to templates/nginx_download_template.conf
diff --git a/templates/traefik.yml b/templates/traefik_compose_template.yml
similarity index 100%
rename from templates/traefik.yml
rename to templates/traefik_compose_template.yml
diff --git a/utils/docker_compose_generator.py b/utils/docker_compose_generator.py
new file mode 100755
index 0000000..30747b1
--- /dev/null
+++ b/utils/docker_compose_generator.py
@@ -0,0 +1,73 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import argparse
+import logging
+# import yaml
+# import ruamel.yaml
+# import json
+
+"""
+docker-compose_generator.py
+
+This method will write a formatted docker-compose.yml for the specified organism (only requires genus and species)
+"""
+
+
+class DockerComposeGenerator:
+
+ def __init__(self):
+ self.mode = None
+ self.genus = None
+ self.species = None
+ self.organism_template = None
+ self.traefik_template = None
+ self.outdir = None
+
+ def generate(self):
+ if self.organism_template is None:
+ self.organism_template = str(os.getcwd() + "/templates/gspecies_compose_template.yml")
+ else:
+ with open(self.organism_template, 'r') as infile:
+ organism_content = list()
+ for line in infile:
+ # Replace placeholders by the genus and species
+ organism_content.append(line.replace("genus_species", str(self.genus.lower() + "_" + self.species)).replace("Genus species", str(self.genus + " " + self.species)).replace("Genus/species", str(self.genus + "/" + self.species)).replace("gspecies", str(self.genus.lower()[0] + self.species)))
+ self.write_yml(content=organism_content)
+
+ if self.traefik_template is None:
+ self.traefik_template = str(os.getcwd() + "/templates/gspecies_compose_template.yml")
+ else:
+ with open(self.traefik_template, 'r') as infile:
+ traefik_content = list()
+ for line in infile:
+ # Replace placeholders by the genus and species
+ traefik_content.append(line.replace("genus_species", str(self.genus.lower() + "_" + self.species)).replace("Genus species", str(self.genus + " " + self.species)).replace("Genus/species", str(self.genus + "/" + self.species)).replace("gspecies", str(self.genus.lower()[0] + self.species)))
+ self.write_yml(content=traefik_content)
+
+ def write_yml(self, content):
+ with open(self.outdir + "/docker-compose.yml", 'w') as outfile:
+ for line in content:
+ outfile.write(line)
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(description="Generator of docker-compose.yml for GGA automated integration "
+ "following the templates available @ "
+ "https://gitlab.inria.fr/abretaud/genodock_demo/")
+ parser.add_argument("-g", "--genus", type=str, help="input genus")
+ parser.add_argument("-s", "--species", type=str, help="input species")
+ parser.add_argument("-o", "--organism-template", type=str, help="input organism template docker-compose.yml (compose or stack), optional")
+ parser.add_argument("-t", "--traefik-template", type=str, help="input organism template docker-compose.yml (compose or stack), optional")
+ parser.add_argument("-m", "--main-dir", type=str, help="where to write the output traefik docker-compose.yml (defaults to cd, autoload places it in main directory)")
+ parser.add_argument("-d", "--organism-dir", type=str, help="where to write the output organism docker-compose.yml (defaults to cd, autoload places it in organism directory)")
+ args = parser.parse_args()
+
+ dc_generator = DockerComposeGenerator()
+ dc_generator.genus = args.genus
+ dc_generator.species = args.species
+ if args.template:
+ dc_generator.template = args.template
+ dc_generator.outdir = args.outdir
+ dc_generator.generate()
diff --git a/utils/metadata_generator.py b/utils/metadata_generator.py
new file mode 100755
index 0000000..c03ff0c
--- /dev/null
+++ b/utils/metadata_generator.py
@@ -0,0 +1,36 @@
+import os
+import logging
+import yaml
+
+"""
+Metadata generator for gga_auto_load
+
+Creates a file that summarizes actions taken by the autoload script (e.g what was done in the dedicated galaxy instance)
+This organism metadata file is located in the metadata directory of the organism directory (i.e /genus_species/metadata)
+By default, will also create/update a general metadata file (located in the parent directory i.e where all the organisms
+directories are located)
+
+TODO: move inside autoload
+
+Metadata format: .yml
+"""
+
+
+class MetadataGenerator:
+
+ def __init__(self, maindir):
+ self.maindir = maindir
+ self.genus = None
+ self.species = None
+ self.metadata = None
+ self.do_update = False
+ self.date = "01/01/2020"
+
+
+ # def read_metadata(self):
+ # for label, content in metadata.items():
+ # print("FOO")
+
+ def write_metadata(self):
+ with open(self.maindir + "/main_metadata.yml", "a") as metadata:
+ metadata.write("\n\nAdded " + self.genus + " " + self.species + "")
\ No newline at end of file
diff --git a/workflows/phaeoexplorer_base_workflow.ga b/workflows/phaeoexplorer_base_workflow.ga
deleted file mode 100644
index 5af63fe..0000000
--- a/workflows/phaeoexplorer_base_workflow.ga
+++ /dev/null
@@ -1 +0,0 @@
-{"uuid": "7ebc1035-728c-4bca-a1c3-abd1c01bc064", "tags": [], "format-version": "0.1", "name": "preset_workflow", "version": 1, "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "6956ef7f-7fec-402b-a8ea-f054a819f351", "label": null}], "input_connections": {}, "tool_state": "{}", "id": 0, "uuid": "74f22d9b-e764-45e4-b0eb-579c9b647ea0", "errors": null, "name": "Input dataset", "label": null, "inputs": [], "position": {"top": 343.433349609375, "left": 201.33331298828125}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "efc230d5-5570-4446-b56b-c0213bef9ef0", "label": null}], "input_connections": {}, "tool_state": "{}", "id": 1, "uuid": "6c1a20fa-828a-404c-b107-76fb8ddf3954", "errors": null, "name": "Input dataset", "label": null, "inputs": [], "position": {"top": 340.41668701171875, 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GitLab