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Merged
merged 2 commits into from
Nov 21, 2025
Merged

minor changes #60

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33773fb
minor changes
sjanssen2 Nov 21, 2025
d3753e7
remove build sections and migrate r to ro
sjanssen2 Nov 21, 2025
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2 changes: 2 additions & 0 deletions Images/redis/start_redis.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,11 @@ cleanup() {
trap cleanup TERM INT

# start two redis server and safe PID in variable
# for user and stats
redis-server --port 7777 &
PY_PID1=$!

# for redbiom
redis-server --port 6379 &
PY_PID2=$!

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51 changes: 21 additions & 30 deletions compose.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ services:
image: postgres:15
container_name: qiita-db
hostname: qiita-db
restart: no
restart: "no"
env_file:
- ./environments/qiita_db.env
environment:
Expand Down Expand Up @@ -35,17 +35,14 @@ services:
- qiita-data:/qiita_data
- server-plugin-configs:/qiita_plugins
- ./logs:/logs
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:r
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:r
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:ro
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:ro
networks:
- qiita-net

qiita:
image: local-qiita:latest
build: # image wird hier direkt gebaut
context: ./Images/qiita
dockerfile: Dockerfile
restart: no
restart: "no"
depends_on:
- qiita-worker
env_file:
Expand All @@ -60,8 +57,8 @@ services:
- qiita-data:/qiita_data
- ./src/qiita:/qiita:U
- ./logs:/logs
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:r
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:r
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:ro
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:ro
- server-plugin-configs:/qiita_plugins
- ./references/qiita_server_certificates:/qiita_certificates
# - ./Images/qiita/start_qiita.sh:/start_qiita.sh
Expand All @@ -73,10 +70,7 @@ services:

qiita-worker:
image: local-qiita:latest
build: # image wird hier direkt gebaut
context: ./Images/qiita
dockerfile: Dockerfile
restart: no
restart: "no"
depends_on:
redis:
condition: service_started
Expand All @@ -93,8 +87,8 @@ services:
volumes:
- qiita-data:/qiita_data
- ./logs:/logs
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:r
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:r
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:ro
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:ro
- server-plugin-configs:/qiita_plugins
- ./references/qiita_server_certificates:/qiita_certificates
- ./src/qiita:/qiita:U
Expand All @@ -106,7 +100,7 @@ services:
replicas: 3
redis:
image: redis:latest
restart: no
restart: "no"
command: ["/start_redis.sh"]
volumes:
- qiita-data:/qiita
Expand Down Expand Up @@ -154,12 +148,9 @@ services:

nginx:
image: local-nginx_qiita:latest
build:
context: ./Images/nginx
dockerfile: Dockerfile
ports:
- "8383:8383"
restart: no
restart: "no"
depends_on:
- qiita
volumes:
Expand All @@ -174,7 +165,7 @@ services:

qtp-biom:
image: local-qtp-biom:latest
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -187,7 +178,7 @@ services:

qtp-sequencing:
image: local-qtp-sequencing:latest
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -199,7 +190,7 @@ services:

qp-target-gene:
image: local-qp-target-gene:latest
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -212,7 +203,7 @@ services:

qtp-visualization:
image: local-qtp-visualization:latest
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -224,7 +215,7 @@ services:

qtp-diversity:
image: local-qtp-diversity:latest
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -236,7 +227,7 @@ services:

qp-deblur:
image: local-qp-deblur:latest
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -250,7 +241,7 @@ services:

qp-qiime2:
image: local-qp-qiime2:latest
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -263,7 +254,7 @@ services:

qtp-job-output-folder:
image: local-qtp-job-output-folder:latest
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -277,11 +268,11 @@ services:
# prior to qiita (master and worker) start up, iterates through the QIITA_PLUGINS : separated list of plugin containers
# to compile all q*.conf files from plugin containers in the server-plugin-configs volume
image: local-plugin_collector
restart: no
restart: "no"
networks:
- qiita-net
volumes:
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:r
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:ro
- server-plugin-configs:/qiita_plugins
- qiita-data:/qiita_data
depends_on:
Expand Down
59 changes: 23 additions & 36 deletions compose_github.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ services:
image: postgres:15
container_name: qiita-db
hostname: qiita-db
restart: no
restart: "no"
env_file:
- ./environments/qiita_db.env
environment:
Expand Down Expand Up @@ -39,18 +39,15 @@ services:
volumes:
- qiita-data:/qiita_data
- server-plugin-configs:/qiita_plugins
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:r
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:r
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:ro
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:ro
- qiita-logs:/logs
networks:
- qiita-net

qiita:
image: ghcr.io/jlab/qiita-keycloak/qiita:testcandidate
build: # image wird hier direkt gebaut
context: ./Images/qiita
dockerfile: Dockerfile
restart: no
restart: "no"
depends_on:
- qiita-worker
env_file:
Expand All @@ -64,8 +61,8 @@ services:
volumes:
- qiita-data:/qiita_data
- qiita-logs:/logs
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:r
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:r
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:ro
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:ro
- server-plugin-configs:/qiita_plugins
- ./references/qiita_server_certificates:/qiita_certificates
- test_tmp_dir:/tmp
Expand All @@ -76,10 +73,7 @@ services:

qiita-worker:
image: ghcr.io/jlab/qiita-keycloak/qiita:testcandidate
build: # image wird hier direkt gebaut
context: ./Images/qiita
dockerfile: Dockerfile
restart: no
restart: "no"
depends_on:
redis:
condition: service_started
Expand All @@ -96,8 +90,8 @@ services:
volumes:
- qiita-data:/qiita_data
- qiita-logs:/logs
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:r
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:r
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:ro
- ./Images/qiita/config_portal.cfg:/qiita_configurations/config_portal.cfg:ro
- server-plugin-configs:/qiita_plugins
- ./references/qiita_server_certificates:/qiita_certificates
- test_tmp_dir:/tmp
Expand All @@ -108,16 +102,12 @@ services:

redis:
image: redis:latest
restart: no
environment:
- PORTSTATS=7777
- PORTREDBIOM=6379
command: >
sh -c "redis-server --port $$PORTSTATS &&
redis-server --port $$PORTREDBIOM"
restart: "no"
command: ["/start_redis.sh"]
volumes:
- qiita-data:/qiita
- qiita-logs:/logs
- ./Images/redis/start_redis.sh:/start_redis.sh
networks:
- qiita-net
# healthcheck:
Expand All @@ -129,12 +119,9 @@ services:

nginx:
image: ghcr.io/jlab/qiita-keycloak/nginx:testcandidate
build:
context: ./Images/nginx
dockerfile: Dockerfile
ports:
- "8383:8383"
restart: no
restart: "no"
depends_on:
- qiita
volumes:
Expand All @@ -156,7 +143,7 @@ services:

qtp-biom:
image: ghcr.io/jlab/qiita-keycloak/qtp-biom:testcandidate
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -168,7 +155,7 @@ services:

qtp-sequencing:
image: ghcr.io/jlab/qiita-keycloak/qtp-sequencing:testcandidate
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -186,7 +173,7 @@ services:

qp-target-gene:
image: ghcr.io/jlab/qiita-keycloak/qp-target-gene:testcandidate
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -199,7 +186,7 @@ services:

qtp-visualization:
image: ghcr.io/jlab/qiita-keycloak/qtp-visualization:testcandidate
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -211,7 +198,7 @@ services:

qtp-diversity:
image: ghcr.io/jlab/qiita-keycloak/qtp-diversity:testcandidate
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -223,7 +210,7 @@ services:

qp-deblur:
image: ghcr.io/jlab/qiita-keycloak/qp-deblur:testcandidate
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -236,7 +223,7 @@ services:

qp-qiime2:
image: ghcr.io/jlab/qiita-keycloak/qp-qiime2:testcandidate
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -249,7 +236,7 @@ services:

qtp-job-output-folder:
image: ghcr.io/jlab/qiita-keycloak/qtp-job-output-folder:testcandidate
restart: no
restart: "no"
volumes:
- qiita-data:/qiita_data
- ./references/qiita_server_certificates:/qiita_server_certificates
Expand All @@ -263,11 +250,11 @@ services:
# prior to qiita (master and worker) start up, iterates through the QIITA_PLUGINS : separated list of plugin containers
# to compile all q*.conf files from plugin containers in the server-plugin-configs volume
image: ghcr.io/jlab/qiita-keycloak/plugin_collector:testcandidate
restart: no
restart: "no"
networks:
- qiita-net
volumes:
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:r
- ./Images/qiita/config_qiita_oidc.cfg:/qiita_configurations/qiita_server.cfg:ro
- server-plugin-configs:/qiita_plugins
- qiita-data:/qiita_data
depends_on:
Expand Down