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docker-compose.yml
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docker-compose.yml
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version: '3'
services:
# Service for the AllegroGraph
allegro:
image: bfrgoncalves/innuendo_docker_allegro:1.0.0
restart: on-failure
expose:
- "10035"
command: ["init_all"]
# Service for the redis queue
redis:
image: redis
expose:
- "6379"
# Service for the INNUENDO frontend. Requires the config files for the
# application and mapping of the fastq files
# bfrgoncalves/innuendo_docker_frontend:1.0.0
frontend:
image: kapsakcj/innuendo_docker_frontend:1.0.0
privileged: true
restart: on-failure
volumes:
- ./configs/app/config_frontend.py:/Frontend/INNUENDO_REST_API/config.py
- user_data:/INNUENDO
- ./inputs/fastq:/INNUENDO/ftp/files
- ./inputs/backups:/INNUENDO/backups
- ./inputs/v1/classifications:/INNUENDO/inputs/v1/classifications
- ./inputs/v1/core_lists:/INNUENDO/inputs/v1/core_lists
- ./inputs/v1/indexes:/INNUENDO/inputs/v1/indexes
- ./inputs/v1/legacy_metadata:/INNUENDO/inputs/v1/legacy_metadata
- ./inputs/v1/legacy_profiles:/INNUENDO/inputs/v1/legacy_profiles
- ./components/Frontend/build_allegro.py:/Frontend/INNUENDO_REST_API/build_allegro.py
- singularity_cache:/mnt/singularity_cache
- /home/pjx8/github-repos/INNUENDO_REST_API/app:/Frontend/INNUENDO_REST_API/app
ports:
- "5000:5000"
depends_on:
- "allegro"
- "db_innuendo"
- "db_mlst"
- "web"
command: ["init_allegro", "build_db", "init_app"]
# DB for the INNUENDO application.
db_innuendo:
image: bfrgoncalves/innuendo_docker_db_innuendo:1.0.0
restart: always
environment:
POSTGRES_USER: "innuendo"
POSTGRES_PASSWORD: "innuendo_database"
POSTGRES_DB: "innuendo"
volumes:
- ./configs/dbs/alembic_drop.sql:/docker-entrypoint-initdb.d/1-schema.sql
# DB for the INNUENDO application.
db_flowcraft:
image: bfrgoncalves/innuendo_docker_db_flowcraft:1.0.0
restart: always
volumes:
- ./configs/flowcraft/config_flowcraft.py:/FlowCraft_inspect/flowcraft-webapp/flowcraft-webapp/flowcraftapp/settings.py
environment:
POSTGRES_USER: "assemblerflow"
POSTGRES_PASSWORD: "assflow"
POSTGRES_DB: "assemblerflow"
# DB for the INNUENDO wgMLST profiles.
db_mlst:
image: bfrgoncalves/innuendo_docker_db_mlst:1.0.0
restart: always
environment:
POSTGRES_USER: "innuendo"
POSTGRES_PASSWORD: "innuendo_database"
POSTGRES_DB: "mlst_database"
volumes:
- ./configs/dbs/alembic_drop.sql:/docker-entrypoint-initdb.d/1-schema.sql
# DB for PHYLOViZ Online.
db_phyloviz:
image: bfrgoncalves/innuendo_docker_db_phyloviz:1.0.0
restart: always
environment:
POSTGRES_USER: "phyloviz"
POSTGRES_PASSWORD: "phyloviz"
POSTGRES_DB: "phyloviz"
volumes:
- ./configs/dbs/init.sql:/docker-entrypoint-initdb.d/1-schema.sql
# Service for PHYLOViZ Online application
# bfrgoncalves/phylovizonline_docker:1.0.0
phyloviz:
image: bfrgoncalves/phylovizonline_docker:1.0.0
restart: on-failure
volumes:
- ./configs/app/phyloviz_config.js:/PHYLOVIZ/Online-PhyloViZ/config.js
expose:
- "80"
depends_on:
- "db_phyloviz"
- "redis"
- "web"
command: ["init_all"]
# Service for FlowCraft web application. Used for the inspect and report
# system
flowcraft:
image: bfrgoncalves/innuendo_docker_flowcraft:1.0.0
restart: on-failure
expose:
- "8000"
volumes:
- ./configs/flowcraft/config_flowcraft.py:/FlowCraft_inspect/flowcraft-webapp/flowcraft-webapp/flowcraftapp/settings.py
- ./configs/flowcraft/config.json:/FlowCraft_inspect/flowcraft-webapp/flowcraft-webapp/frontend/config.json
depends_on:
- "db_flowcraft"
- "web"
command: ["init_all"]
# Service for the INNUENDO frontend. Requires the config files for the
# application and mapping of the fastq files. It also requires the slurm
# conf files.
controller:
image: kapsakcj/innuendo_docker_controller:1.0.0
command: ["slurmctld", "get_schemas"]
container_name: slurmctld
hostname: slurmctld
privileged: true
tty: true
#restart: on-failure
volumes:
- etc_munge:/etc/munge
- etc_slurm:/etc/slurm
- ./components/Controller/slurm.conf:/etc/slurm/slurm.conf
- slurm_jobdir:/data
- var_log_slurm:/var/log/slurm
- ./configs/app/config_process.py:/Controller/INNUENDO_PROCESS_CONTROLLER/config.py
- ./configs/nextflow/nextflow.config:/Controller/flowcraft/flowcraft/nextflow.config
- user_data:/INNUENDO
- ./inputs/fastq:/INNUENDO/ftp/files
- ./inputs/v1/schemas:/INNUENDO/inputs/v1/schemas
- ./inputs/prodigal_training_files:/INNUENDO/inputs/prodigal_training_files
- ./inputs/v1/core_lists:/INNUENDO/inputs/v1/core_lists
- ./inputs/serotyping_files:/INNUENDO/inputs/serotyping_files
- singularity_cache:/mnt/singularity_cache
expose:
- "6817"
- "5001"
depends_on:
- "slurmdbd"
- "allegro"
- "frontend"
- "web"
# service with mysql database for slurm accounting
mysql:
image: mysql:5.7
hostname: mysql
container_name: mysql
privileged: true
environment:
MYSQL_RANDOM_ROOT_PASSWORD: "yes"
MYSQL_DATABASE: slurm_acct_db
MYSQL_USER: slurm
MYSQL_PASSWORD: password
volumes:
- var_lib_mysql:/var/lib/mysql
# service for the the SLURM dbd.
slurmdbd:
image: bfrgoncalves/innuendo_docker_controller:1.0.0
command: ["slurmdbd"]
container_name: slurmdbd
hostname: slurmdbd
privileged: true
volumes:
- etc_munge:/etc/munge
- etc_slurm:/etc/slurm
- ./components/Controller/slurm.conf:/etc/slurm/slurm.conf
- var_log_slurm:/var/log/slurm
- singularity_cache:/mnt/singularity_cache
expose:
- "6819"
depends_on:
- "mysql"
# service for slurm computing node 1
c1:
image: bfrgoncalves/innuendo_docker_controller:1.0.0
command: ["slurmd"]
hostname: c1
container_name: c1
privileged: true
volumes:
- etc_munge:/etc/munge
- etc_slurm:/etc/slurm
- ./components/Controller/slurm.conf:/etc/slurm/slurm.conf
- slurm_jobdir:/data
- var_log_slurm:/var/log/slurm
- singularity_cache:/mnt/singularity_cache
- user_data:/INNUENDO
- ./inputs/fastq:/INNUENDO/ftp/files
- ./inputs/v1/schemas:/INNUENDO/inputs/v1/schemas
- ./inputs/prodigal_training_files:/INNUENDO/inputs/prodigal_training_files
- ./inputs/v1/core_lists:/INNUENDO/inputs/v1/core_lists
- ./inputs/serotyping_files:/INNUENDO/inputs/serotyping_files
expose:
- "6818"
depends_on:
- "controller"
# service for slurm computing node 2
c2:
image: bfrgoncalves/innuendo_docker_controller:1.0.0
command: ["slurmd"]
hostname: c2
container_name: c2
privileged: true
volumes:
- etc_munge:/etc/munge
- etc_slurm:/etc/slurm
- ./components/Controller/slurm.conf:/etc/slurm/slurm.conf
- slurm_jobdir:/data
- var_log_slurm:/var/log/slurm
- singularity_cache:/mnt/singularity_cache
- user_data:/INNUENDO
- ./inputs/fastq:/INNUENDO/ftp/files
- ./inputs/v1/schemas:/INNUENDO/inputs/v1/schemas
- ./inputs/prodigal_training_files:/INNUENDO/inputs/prodigal_training_files
- ./inputs/v1/core_lists:/INNUENDO/inputs/v1/core_lists
- ./inputs/serotyping_files:/INNUENDO/inputs/serotyping_files
expose:
- "6818"
depends_on:
- "controller"
# Service for the nginx web server. it requires mapping of the nginx conf
# to be able to access all the other processes from the browser.
web:
image: nginx:latest
restart: on-failure
volumes:
- ./configs/nginx/site.conf:/etc/nginx/conf.d/default.conf
- static-content:/usr/src/app
- ./configs/app/config_reports.js:/usr/src/app/config.js
- flowcraft-content:/usr/src/flowcraft
ports:
- "80:80"
- "82:82"
- "10035:10035"
volumes:
static-content:
flowcraft-content:
etc_munge:
etc_slurm:
slurm_jobdir:
var_lib_mysql:
var_log_slurm:
singularity_cache:
user_data: