From 139db9f1810293f15379ca5b784c637b71294d62 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Thu, 15 Apr 2021 11:13:16 +0200
Subject: [PATCH] removed backup gspecies template file, precisions for
required/optional parameters in config_example.yml
---
examples/config_example.yml | 28 +-
templates/gspecies_compose_template.yml.bak | 303 --------------------
2 files changed, 14 insertions(+), 317 deletions(-)
delete mode 100644 templates/gspecies_compose_template.yml.bak
diff --git a/examples/config_example.yml b/examples/config_example.yml
index 6f22504..4d566ce 100644
--- a/examples/config_example.yml
+++ b/examples/config_example.yml
@@ -2,25 +2,25 @@
# "all" section contains variables used by several services at once or the paths to import sensitive files
all:
- hostname: localhost # The hosting machine name
- dashboard_port: 8001 # The desired port (on the hosting machine) for the traefik container dashboard
- http_port: 8888 # The HTTP port docker will use on the hosting machine
- https_port: 8889 # Optional. The HTTPS port docker will use on the hosting machine. Required for Authelia
- proxy_ip: XXXXXXXXXXXX # IP of the upstream proxy (used by Traefik)
- authentication_domain_name: XXXXXXXXXXXX # Optional. Required for Authelia. The authentication domain name.
- authelia_config_path: /path/to/authelia_config.yml # Optional. Required for Authelia. Path to the Authelia configuration file
+ hostname: localhost # Required. The hosting machine name
+ dashboard_port: 8001 # Required. The desired port (on the hosting machine) for the traefik container dashboard
+ http_port: 8888 # Required. The HTTP port docker will use on the hosting machine
+ https_port: 8889 # Required for Authelia. The HTTPS port docker will use on the hosting machine
+ proxy_ip: XXXXXXXXXXXX # Required. IP of the upstream proxy (used by Traefik)
+ authentication_domain_name: XXXXXXXXXXXX # Required for Authelia. The authentication domain name.
+ authelia_config_path: /path/to/authelia_config.yml # Required for Authelia. Path to the Authelia configuration file
# galaxy-specific variables
galaxy:
- galaxy_default_admin_email: gga@galaxy.org
- galaxy_defaut_admin_user: gga
- galaxy_default_admin_password: password
- webapollo_user: admin_apollo@galaxy.org
- webapollo_password: apollopass
- galaxy_config_remote_user_maildomain: mydomain.com # The maildomain used by Galaxy authentication
+ galaxy_default_admin_email: gga@galaxy.org # Required
+ galaxy_defaut_admin_user: gga # Required
+ galaxy_default_admin_password: password # Required
+ webapollo_user: admin_apollo@galaxy.org # Required
+ webapollo_password: apollopass # Required
+ galaxy_config_remote_user_maildomain: mydomain.com # Required. The maildomain used by Galaxy authentication
persist_galaxy_data: "True" # Optional. If True, docker data will be backed up. Do not set this variable to "false" for production
# tripal-specific variables
tripal:
- tripal_password: tripalpass # Tripal database password (also used by galaxy as an environment variable)
+ tripal_password: tripalpass # Required. Tripal database password (also used by galaxy as an environment variable)
banner_path: /my/path/banner.png # Optional. Custom banner path
tripal_theme_name: tripal_gga # Optional. Use this to use another theme
tripal_theme_git_clone: http://gitlab.sb-roscoff.fr/abims/e-infra/tripal_gga.git # Optional. Use this to install another theme.
diff --git a/templates/gspecies_compose_template.yml.bak b/templates/gspecies_compose_template.yml.bak
deleted file mode 100644
index da6d645..0000000
--- a/templates/gspecies_compose_template.yml.bak
+++ /dev/null
@@ -1,303 +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(`custom_host`) && 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: "custom_theme" # Use this to use another theme
- THEME_GIT_CLONE: "custom_git_clone" # Use this to install another theme
- ADMIN_PASSWORD: custom_tripal_admin_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(`custom_host`) && 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: "custom_galaxy_default_admin_email"
- GALAXY_DEFAULT_ADMIN_USER: "custom_galaxy_defaut_admin_user"
- GALAXY_DEFAULT_ADMIN_PASSWORD: "custom_galaxy_default_admin_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: "custom_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: custom_galaxy_tripal_password # See tripal config above
- GALAXY_WEBAPOLLO_URL: http://one-of-the-swarm-node:8888/apollo/
- GALAXY_WEBAPOLLO_USER: "custom_galaxy_web_apollo_user"
- GALAXY_WEBAPOLLO_PASSWORD: "custom_galaxy_web_apollo_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(`custom_host`) && 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(`custom_host`) && 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(`custom_host`) && 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
--
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