From 33773fb1016ff0e0dbf06720a0a338da416e9923 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 21 Nov 2025 11:26:40 +0100 Subject: [PATCH 1/2] minor changes --- Images/redis/start_redis.sh | 2 ++ compose.yaml | 28 ++++++++++++++-------------- compose_github.yaml | 36 ++++++++++++++++-------------------- 3 files changed, 32 insertions(+), 34 deletions(-) diff --git a/Images/redis/start_redis.sh b/Images/redis/start_redis.sh index 7fd00f7..9f24e57 100755 --- a/Images/redis/start_redis.sh +++ b/Images/redis/start_redis.sh @@ -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=$! +# for redbiom redis-server --port 6379 & PY_PID2=$! diff --git a/compose.yaml b/compose.yaml index b1870dc..d4af173 100644 --- a/compose.yaml +++ b/compose.yaml @@ -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: @@ -45,7 +45,7 @@ services: build: # image wird hier direkt gebaut context: ./Images/qiita dockerfile: Dockerfile - restart: no + restart: "no" depends_on: - qiita-worker env_file: @@ -76,7 +76,7 @@ services: build: # image wird hier direkt gebaut context: ./Images/qiita dockerfile: Dockerfile - restart: no + restart: "no" depends_on: redis: condition: service_started @@ -106,7 +106,7 @@ services: replicas: 3 redis: image: redis:latest - restart: no + restart: "no" command: ["/start_redis.sh"] volumes: - qiita-data:/qiita @@ -159,7 +159,7 @@ services: dockerfile: Dockerfile ports: - "8383:8383" - restart: no + restart: "no" depends_on: - qiita volumes: @@ -174,7 +174,7 @@ services: qtp-biom: image: local-qtp-biom:latest - restart: no + restart: "no" volumes: - qiita-data:/qiita_data - ./references/qiita_server_certificates:/qiita_server_certificates @@ -187,7 +187,7 @@ services: qtp-sequencing: image: local-qtp-sequencing:latest - restart: no + restart: "no" volumes: - qiita-data:/qiita_data - ./references/qiita_server_certificates:/qiita_server_certificates @@ -199,7 +199,7 @@ 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 @@ -212,7 +212,7 @@ services: qtp-visualization: image: local-qtp-visualization:latest - restart: no + restart: "no" volumes: - qiita-data:/qiita_data - ./references/qiita_server_certificates:/qiita_server_certificates @@ -224,7 +224,7 @@ services: qtp-diversity: image: local-qtp-diversity:latest - restart: no + restart: "no" volumes: - qiita-data:/qiita_data - ./references/qiita_server_certificates:/qiita_server_certificates @@ -236,7 +236,7 @@ services: qp-deblur: image: local-qp-deblur:latest - restart: no + restart: "no" volumes: - qiita-data:/qiita_data - ./references/qiita_server_certificates:/qiita_server_certificates @@ -250,7 +250,7 @@ services: qp-qiime2: image: local-qp-qiime2:latest - restart: no + restart: "no" volumes: - qiita-data:/qiita_data - ./references/qiita_server_certificates:/qiita_server_certificates @@ -263,7 +263,7 @@ 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 @@ -277,7 +277,7 @@ 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: diff --git a/compose_github.yaml b/compose_github.yaml index 0a75348..92f4476 100644 --- a/compose_github.yaml +++ b/compose_github.yaml @@ -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: @@ -50,7 +50,7 @@ services: build: # image wird hier direkt gebaut context: ./Images/qiita dockerfile: Dockerfile - restart: no + restart: "no" depends_on: - qiita-worker env_file: @@ -79,7 +79,7 @@ services: build: # image wird hier direkt gebaut context: ./Images/qiita dockerfile: Dockerfile - restart: no + restart: "no" depends_on: redis: condition: service_started @@ -108,16 +108,12 @@ 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: @@ -134,7 +130,7 @@ services: dockerfile: Dockerfile ports: - "8383:8383" - restart: no + restart: "no" depends_on: - qiita volumes: @@ -156,7 +152,7 @@ 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 @@ -168,7 +164,7 @@ 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 @@ -186,7 +182,7 @@ 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 @@ -199,7 +195,7 @@ 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 @@ -211,7 +207,7 @@ 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 @@ -223,7 +219,7 @@ 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 @@ -236,7 +232,7 @@ 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 @@ -249,7 +245,7 @@ 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 @@ -263,7 +259,7 @@ 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: From d3753e76e185a99aae059d51802803c712abc6c5 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 21 Nov 2025 11:30:55 +0100 Subject: [PATCH 2/2] remove build sections and migrate r to ro --- compose.yaml | 23 +++++++---------------- compose_github.yaml | 23 +++++++---------------- 2 files changed, 14 insertions(+), 32 deletions(-) diff --git a/compose.yaml b/compose.yaml index d4af173..e7d0ce2 100644 --- a/compose.yaml +++ b/compose.yaml @@ -35,16 +35,13 @@ 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" depends_on: - qiita-worker @@ -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 @@ -73,9 +70,6 @@ services: qiita-worker: image: local-qiita:latest - build: # image wird hier direkt gebaut - context: ./Images/qiita - dockerfile: Dockerfile restart: "no" depends_on: redis: @@ -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 @@ -154,9 +148,6 @@ services: nginx: image: local-nginx_qiita:latest - build: - context: ./Images/nginx - dockerfile: Dockerfile ports: - "8383:8383" restart: "no" @@ -281,7 +272,7 @@ services: 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: diff --git a/compose_github.yaml b/compose_github.yaml index 92f4476..083ff59 100644 --- a/compose_github.yaml +++ b/compose_github.yaml @@ -39,17 +39,14 @@ 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" depends_on: - qiita-worker @@ -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 @@ -76,9 +73,6 @@ services: qiita-worker: image: ghcr.io/jlab/qiita-keycloak/qiita:testcandidate - build: # image wird hier direkt gebaut - context: ./Images/qiita - dockerfile: Dockerfile restart: "no" depends_on: redis: @@ -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 @@ -125,9 +119,6 @@ services: nginx: image: ghcr.io/jlab/qiita-keycloak/nginx:testcandidate - build: - context: ./Images/nginx - dockerfile: Dockerfile ports: - "8383:8383" restart: "no" @@ -263,7 +254,7 @@ services: 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: