Merge pull request #60 from jlab/fix_compose

minor changes

Author: sjanssen2

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=$!
 

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:
@@ -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:
@@ -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
@@ -73,10 +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
@@ -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
@@ -106,7 +100,7 @@ services:
         replicas: 3
   redis:
     image: redis:latest
-    restart: no
+    restart: "no"
     command: ["/start_redis.sh"]
     volumes:
       - qiita-data:/qiita
@@ -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:
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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:

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:
@@ -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:
@@ -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
@@ -76,10 +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
@@ -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
@@ -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:
@@ -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:
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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: