From 8fa6a46e64448e979b4841d5f60f7cb38ed19bc1 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Mon, 10 Aug 2020 15:08:37 +0200
Subject: [PATCH] Swarm functional version (wait for galaxy service to finish
scanning /export before running the data loading + workflow script)
---
.idea/gga_load_data.iml | 9 ++
.idea/misc.xml | 4 +
.idea/modules.xml | 8 ++
.../docker_compose_generator.cpython-38.pyc | Bin 2631 -> 2644 bytes
__pycache__/metadata_generator.cpython-38.pyc | Bin 895 -> 908 bytes
__pycache__/table_parser.cpython-38.pyc | Bin 2681 -> 2694 bytes
autoload.py | 72 ++++++-----
examples/phaeoexplorer_test.json | 28 +++++
templates/stack-organism.yml | 112 +++++++++---------
9 files changed, 145 insertions(+), 88 deletions(-)
create mode 100644 .idea/gga_load_data.iml
create mode 100644 .idea/misc.xml
create mode 100644 .idea/modules.xml
create mode 100644 examples/phaeoexplorer_test.json
diff --git a/.idea/gga_load_data.iml b/.idea/gga_load_data.iml
new file mode 100644
index 0000000..35bc48c
--- /dev/null
+++ b/.idea/gga_load_data.iml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+ <component name="NewModuleRootManager">
+ <content url="file://$MODULE_DIR$" />
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" name="R Skeletons" level="application" />
+ </component>
+</module>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000..a2e120d
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.7" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000..aae5791
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectModuleManager">
+ <modules>
+ <module fileurl="file://$PROJECT_DIR$/.idea/gga_load_data.iml" filepath="$PROJECT_DIR$/.idea/gga_load_data.iml" />
+ </modules>
+ </component>
+</project>
\ No newline at end of file
diff --git a/__pycache__/docker_compose_generator.cpython-38.pyc b/__pycache__/docker_compose_generator.cpython-38.pyc
index 8b1e7192a80732d100114a7d05437f34e9ec1cdd..3519791c440b492aee228a3785e1d32a58d2896a 100644
GIT binary patch
delta 40
ucmX>uaz%tYl$V!_0SLqtR5o&RGcl%37H2ZyNGvVM&&f|r+3d!|$N>PZ1ql}b
delta 31
lcmca2a$JNvl$V!_0SK%oNp9rkW@3z-EY4)IIfCgAI{<E`2SES;
diff --git a/__pycache__/metadata_generator.cpython-38.pyc b/__pycache__/metadata_generator.cpython-38.pyc
index ad192f7b2aec5dd419e9f25e1c292687667b5788..eed2e9474897c4805dc636277bafade56ab8a337 100644
GIT binary patch
delta 40
ucmey**2B&n%FD~e00d$RDjT_785t8M2Qr#)B$k%s=j11*Y;Iuu&j<jsD+-7J
delta 31
lcmeBS|Ifx9%FD~e00fNJ<u-D=GBO5F4rDahJc;oaBLHt#2g3jW
diff --git a/__pycache__/table_parser.cpython-38.pyc b/__pycache__/table_parser.cpython-38.pyc
index 1d26775d084d79ee19760b3121f42c0a6107b416..906e86c557512b57afb6d437208935bfd7159922 100644
GIT binary patch
delta 40
ucmew<(k99s%FD~e00d$RDjT`InHZxchclUQB$k%s=j11*Y;I%v%nksyB?_Sc
delta 31
lcmZn@{VBp7%FD~e00bA0$Zh2IW@7Z69L{92c?Q!vb^w0X2$=u?
diff --git a/autoload.py b/autoload.py
index 50d880f..5041385 100755
--- a/autoload.py
+++ b/autoload.py
@@ -30,7 +30,7 @@ TODO EOSC/Cloudification:
- keep in mind
- divide into 2 general-use scripts
- create docker stack via swarm
- - load data into libraries
+ - load data into libraries (method to load it at init, and a method/script to load it separately (galaxy_data_libs_SI does this already?)
STEPS:
- read input (xls or json)
@@ -49,7 +49,6 @@ STEPS:
class Autoload:
"""
Autoload class contains attributes and functions to interact with GGA
-
"""
def __init__(self, species_parameters_dictionary, args):
@@ -85,19 +84,19 @@ class Autoload:
self.workflow_name = None
self.docker_compose_generator = None
self.metadata = dict()
- self.source_data_dir = "/projet/sbr/phaeoexplorer" # directory/subdirectories where source data files are located
+ self.source_data_dir = "/projet/sbr/phaeoexplorer"
+ # Directory/subdirectories where data files are located (fasta, gff, ...), point to a directory as close as possible to the source files
self.do_update = False
+ # Update the instance (in histories corresponding to the input) instead of creating a new one TODO: move this variable inside methods
+ self.api_key = "dev"
+ # Api key used to communicate with the galaxy instance. Set to "dev" for the moment TODO: find a way to create, store then use the api key safely
def connect_to_instance(self):
"""
Test the connection to the galaxy instance for the current organism
Exit if we can't connect to the instance
"""
- self.instance = galaxy.GalaxyInstance(url=self.instance_url,
- key="ec601ea5005766e1bc106e69ad8b9eaa",
- email="alebars@sb-roscoff.fr",
- password="pouet",
- verify=True)
+ self.instance = galaxy.GalaxyInstance(url=self.instance_url, key=self.api_key)
logging.info("connection to the galaxy instance ...")
try:
self.instance.histories.get_histories()
@@ -108,7 +107,6 @@ class Autoload:
else:
logging.info("successfully connected to galaxy instance @ " + self.instance_url)
-
def get_source_data(self, max_depth):
"""
OBSOLETE
@@ -194,42 +192,54 @@ class Autoload:
# Hard coded paths (find a way to get the files by adding an attribute "path_to_repo")
# Write with string?
- stack_template_path = "/home/fr2424/sib/alebars/PycharmProjects/ggauto/gga_load_data/templates/stack-organism.yml"
- traefik_template_path = "/home/fr2424/sib/alebars/PycharmProjects/ggauto/gga_load_data/templates/traefik.yml"
- authelia_config_path = "/home/fr2424/sib/alebars/PycharmProjects/ggauto/gga_load_data/templates/authelia_config.yml"
- authelia_users_path = "/home/fr2424/sib/alebars/PycharmProjects/ggauto/gga_load_data/templates/authelia_users.yml"
+ stack_template_path = self.script_dir + "/templates/stack-organism.yml"
+ traefik_template_path = self.script_dir + "/templates/traefik.yml"
+ authelia_config_path = self.script_dir + "/templates/authelia_config.yml"
+ authelia_users_path = self.script_dir + "/templates/authelia_users.yml"
+
+ if self.sex and self.strain:
+ genus_species_strain_sex = self.genus.lower() + "_" + self.species + "_" + self.strain + "_" + self.sex
+ else:
+ genus_species_strain_sex = self.genus.lower() + "_" + self.species
with open(stack_template_path, '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)))
+ 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)).replace("genus_species_strain_sex", genus_species_strain_sex))
with open("./docker-compose.yml", 'w') as outfile:
for line in organism_content:
outfile.write(line)
+ subprocess.call(["python3", self.script_dir + "/create_mounts.py"], cwd=working_dir)
try:
os.mkdir("../traefik")
os.mkdir("../traefik/authelia")
+ shutil.copy(authelia_config_path, "../traefik/authelia/configuration.yml")
+ shutil.copy(authelia_users_path, "../traefik/authelia/users.yml")
+ # with open(traefik_template_path, 'r') as infile:
+ # traefik_content = list()
+ # for line in infile:
+ # # Replace placeholders by the genus and species (there are none)
+ # 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)).replace("genus_species_strain_sex", genus_species_strain_sex))
+ # with open("../traefik/docker-compose.yml", 'w') as outfile:
+ # for line in traefik_content:
+ # outfile.write(line)
+ subprocess.call(["python3", self.script_dir + "/create_mounts.py"], cwd=working_dir)
except FileExistsError:
- logging.debug("traefik directory already exists")
+ logging.debug("SKIP: Traefik directory already exists")
- with open(traefik_template_path, '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)))
- with open("../traefik/docker-compose.yml", 'w') as outfile:
- for line in traefik_content:
- outfile.write(line)
- shutil.copy(authelia_config_path, "../traefik/authelia/configuration.yml")
- shutil.copy(authelia_users_path, "../traefik/authelia/users.yml")
+
+ # Create volumes for the containers (script written by A. Bretaudeau)
+ subprocess.call(["python3", self.script_dir + "/create_mounts.py"], cwd=working_dir)
+
# Find all files in source_data directory, to link the matching files in the src_data dir tree
# Can be turned into a generator for performance
+ # TODO: cp data files method in a separate function (for EOSC)
for dirpath, dirnames, files in os.walk(self.source_data_dir):
if "0" in str(dirpath): # ensures to take the correct files (other dirs hold files with the correct names, but I don't know if they are the same
for f in files:
@@ -257,14 +267,13 @@ class Autoload:
except TypeError:
pass
- # Launch and update docker stacks (cf docs)
- deploy_script_path = self.script_dir + "/deploy.sh"
- subprocess.call(["sh", deploy_script_path, self.genus_species])
-
-
+ # Launch and update docker stacks (cf docs) TODO: deploy method in a separate function (for EOSC)
+ # deploy_script_path = self.script_dir + "/deploy.sh"
+ # subprocess.call(["sh", deploy_script_path, self.genus_species])
def write_nginx_conf(self):
"""
+ OBSOLETE: compose method
Generate (and update nginx) conf files to add new organisms from the proxy
:return:
@@ -273,7 +282,6 @@ class Autoload:
nginx_organism_path = "" # nginx conf template for the current organism (used once)
docker_proxy_template_path = "" # dockerfile for the main proxy (used once)
-
def modify_fasta_headers(self):
"""
Change the fasta headers before integration.
diff --git a/examples/phaeoexplorer_test.json b/examples/phaeoexplorer_test.json
new file mode 100644
index 0000000..abf3792
--- /dev/null
+++ b/examples/phaeoexplorer_test.json
@@ -0,0 +1,28 @@
+[
+ {
+ "genus" : "Ectocarpus",
+ "species" : "sp1",
+ "common" : "",
+ "strain" : "",
+ "sex" : "male",
+ "origin" : "Unknown",
+ "version" : "1.0",
+ "performed by" : "Genoscope",
+ "genome version" : "1.0",
+ "ogs version" : "1.0",
+ "date" : "2020-08-03"
+ },
+ {
+ "genus" : "Ectocarpus",
+ "species" : "sp2",
+ "common" : "",
+ "strain" : "",
+ "sex" : "male",
+ "origin" : "Unknown",
+ "version" : "1.0",
+ "performed by" : "Genoscope",
+ "genome version" : "1.0",
+ "ogs version" : "1.0",
+ "date" : "2020-08-03"
+ }
+]
diff --git a/templates/stack-organism.yml b/templates/stack-organism.yml
index 9cc4a4b..0e20fe9 100644
--- a/templates/stack-organism.yml
+++ b/templates/stack-organism.yml
@@ -10,17 +10,17 @@ services:
- ./nginx/conf:/etc/nginx/conf.d
networks:
- traefikbig
- - genus_species_1a
+ - genus_species
deploy:
labels:
# Download page
- - "traefik.http.routers.genus_species_1a-nginx.rule=(Host(`scratchgmodv1`) && PathPrefix(`/sp/genus_species_1a/download`))"
-# - "traefik.http.routers.genus_species_1a-nginx.tls=true"
-# - "traefik.http.routers.genus_species_1a-nginx.entryPoints=webs"
- - "traefik.http.routers.genus_species_1a-nginx.entryPoints=web" # lg
-# - "traefik.http.routers.genus_species_1a-nginx.middlewares=sp-auth,sp-app-trailslash,sp-prefix"
- - "traefik.http.routers.genus_species_1a-nginx.middlewares=sp-app-trailslash,sp-prefix" # lg
- - "traefik.http.services.genus_species_1a-nginx.loadbalancer.server.port=80"
+ - "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
@@ -38,16 +38,16 @@ services:
- ./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_1a
- BASE_URL_PATH: /sp/genus_species_1a
+ 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_1a
- ENABLE_JBROWSE: /jbrowse/?data=data/genus_species_1a_ec863_female
+ ELASTICSEARCH_HOST: elasticsearch.genus_species
+ ENABLE_JBROWSE: /jbrowse/?data=data/genus_species_strain_sex
ENABLE_APOLLO: 0
ENABLE_BLAST: 1
ENABLE_DOWNLOAD: 1
@@ -57,19 +57,19 @@ services:
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
+ 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_1a
+ - genus_species
deploy:
labels:
- - "traefik.http.routers.genus_species_1a-tripal.rule=(Host(`scratchgmodv1`) && PathPrefix(`/sp/genus_species_1a`))"
-# - "traefik.http.routers.genus_species_1a-tripal.tls=true"
-# - "traefik.http.routers.genus_species_1a-tripal.entryPoints=webs"
- - "traefik.http.routers.genus_species_1a-tripal.entryPoints=web" # lg
-# - "traefik.http.routers.genus_species_1a-tripal.middlewares=sp-auth,sp-trailslash,sp-prefix,tripal-addprefix"
- - "traefik.http.routers.genus_species_1a-tripal.middlewares=sp-trailslash,sp-prefix,tripal-addprefix" # lg
- - "traefik.http.services.genus_species_1a-tripal.loadbalancer.server.port=80"
+ - "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
@@ -86,7 +86,7 @@ services:
volumes:
- ./docker_data/tripal_db/:/var/lib/postgresql/data/
networks:
- - genus_species_1a
+ - genus_species
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:6.6.1
@@ -107,7 +107,7 @@ services:
ES_JAVA_OPTS: "-Xms500m -Xmx500m"
TAKE_FILE_OWNERSHIP: "true"
networks:
- - genus_species_1a
+ - genus_species
galaxy:
image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod
@@ -127,34 +127,34 @@ services:
GALAXY_CONFIG_USE_REMOTE_USER: "True"
GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "sb-roscoff.fr"
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: "dev"
ENABLE_FIX_PERMS: 0
- PROXY_PREFIX: /sp/genus_species_1a/galaxy
- GALAXY_TRIPAL_URL: http://tripal.genus_species_1a/tripal/
+ 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_1a
+ 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: ""
- GALAXY_CONFIG_MASTER_API_KEY: "dev"
BLAT_ENABLED: 1
networks:
- traefikbig
- - genus_species_1a
+ - genus_species
deploy:
labels:
- - "traefik.http.routers.genus_species_1a-galaxy.rule=(Host(`scratchgmodv1`) && PathPrefix(`/sp/genus_species_1a/galaxy`))"
-# - "traefik.http.routers.genus_species_1a-galaxy.tls=true"
-# - "traefik.http.routers.genus_species_1a-galaxy.entryPoints=webs"
- - "traefik.http.routers.genus_species_1a-galaxy.entryPoints=web" #lg
-# - "traefik.http.routers.genus_species_1a-galaxy.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
- - "traefik.http.routers.genus_species_1a-galaxy.middlewares=sp-app-trailslash,sp-app-prefix" #lg
- - "traefik.http.services.genus_species_1a-galaxy.loadbalancer.server.port=80"
+ - "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
@@ -170,16 +170,16 @@ services:
- ./docker_data/jbrowse/:/jbrowse/data/:ro
networks:
- traefikbig
- - genus_species_1a
+ - genus_species
deploy:
labels:
- - "traefik.http.routers.genus_species_1a-jbrowse.rule=(Host(`scratchgmodv1`) && PathPrefix(`/sp/genus_species_1a/jbrowse`))"
-# - "traefik.http.routers.genus_species_1a-jbrowse.tls=true"
-# - "traefik.http.routers.genus_species_1a-jbrowse.entryPoints=webs"
- - "traefik.http.routers.genus_species_1a-jbrowse.entryPoints=web" # lg
-# - "traefik.http.routers.genus_species_1a-jbrowse.middlewares=sp-auth,sp-app-trailslash,sp-app-prefix"
- - "traefik.http.routers.genus_species_1a-jbrowse.middlewares=sp-app-trailslash,sp-app-prefix" #lg
- - "traefik.http.services.genus_species_1a-jbrowse.loadbalancer.server.port=80"
+ - "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
@@ -191,7 +191,7 @@ services:
depends_on:
- blast-db
environment:
- DB_HOST: blast-db.genus_species_1a
+ DB_HOST: blast-db.genus_species
UPLOAD_LIMIT: 20M
MEMORY_LIMIT: 128M
DB_NAME: 'postgres'
@@ -205,7 +205,7 @@ services:
#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_1a/blast/'
+ 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
@@ -226,16 +226,16 @@ services:
#- /etc/munge/:/etc/munge/:ro
networks:
- traefikbig
- - genus_species_1a
+ - genus_species
deploy:
labels:
- - "traefik.http.routers.genus_species_1a-blast.rule=(Host(`scratchgmodv1`) && PathPrefix(`/sp/genus_species_1a/blast`))"
-# - "traefik.http.routers.genus_species_1a-blast.tls=true"
-# - "traefik.http.routers.genus_species_1a-blast.entryPoints=webs"
- - "traefik.http.routers.genus_species_1a-blast.entryPoints=web" # lg
-# - "traefik.http.routers.genus_species_1a-blast.middlewares=sp-big-req,sp-auth,sp-app-trailslash,sp-app-prefix"
- - "traefik.http.routers.genus_species_1a-blast.middlewares=sp-big-req,sp-app-trailslash,sp-app-prefix" # lg
- - "traefik.http.services.genus_species_1a-blast.loadbalancer.server.port=80"
+ - "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
@@ -251,7 +251,7 @@ services:
volumes:
- ./docker_data/blast_db/:/var/lib/postgresql/data/
networks:
- - genus_species_1a
+ - genus_species
# wiki:
# image: quay.io/abretaud/mediawiki
@@ -294,6 +294,6 @@ services:
networks:
traefikbig:
external: true
- genus_species_1a:
+ genus_species:
driver: overlay
- name: genus_species_1a
+ name: genus_species
--
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