fix ci

.env.example

@@ -1,5 +1,8 @@
-# Release version e.g. 2022q2 or simply latest
-RELEASE=2024q1
+# Select flavor: care, research, dev
+FLAVOR=care
+
+# Release version e.g. 2024q4 or simply latest
+RELEASE=2024q4
 
 # Network configuration
 PORT=8080

.github/workflows/docker-build-dev.yml

@@ -18,9 +18,9 @@ jobs:
 
       - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
       - name: Build dev containers
-        run: docker compose -f compose-dev.yml build cbioportal
+        run: FLAVOR=dev docker compose build cbioportal
       - name: Build dev cbioproxy
-        run: docker compose -f compose-dev.yml build cbioproxy
+        run: FLAVOR=dev docker compose build cbioproxy
       - name: Login to Docker registry
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
         uses: docker/login-action@v3
@@ -30,7 +30,7 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Push cbioportal
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
-        run: docker compose -f compose-dev.yml build cbioportal --push
+        run: FLAVOR=dev docker compose build cbioportal --push
       - name: Push cbioproxy
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
-        run: docker compose -f compose-dev.yml build cbioproxy --push
+        run: FLAVOR=dev docker compose build cbioproxy --push

.github/workflows/docker-build-research.yml

@@ -11,6 +11,6 @@ jobs:
       - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - name: Build research containers
-        run: docker compose -f compose-research.yml build cbioportal
+        run: FLAVOR=research docker compose build cbioportal
       - name: Build research cbioproxy
-        run: docker compose -f compose-research.yml build cbioproxy
+        run: FLAVOR=research docker compose build cbioproxy

.github/workflows/docker-build.yml

@@ -11,6 +11,6 @@ jobs:
       - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
 
       - name: Build care cBioPortal
-        run: docker compose -f compose.yml build cbioportal
+        run: FLAVOR=care docker compose build cbioportal
       - name: Build care cbioproxy
-        run: docker compose -f compose.yml build cbioproxy
+        run: FLAVOR=care docker compose build cbioproxy

README.md

@@ -10,7 +10,7 @@ Installation is described [here](./INSTALL.md)
 
 All images with a `ghcr.io/buschlab/` prefix can be rebuilt using the following command:
 ```
-sudo docker compose -f compose-dev.yml build <service>
+FLAVOR=dev docker compose build <service>
 ```
 
 Such are marked in the table down below.
@@ -53,7 +53,7 @@ The only part that needs a database backup is the HAPI FHIR server. For that ple
 
 ## Ports
 
-| Service | Path (behind OpenResty) | Port (compose-dev.yml) | Image |
+| Service | Path (behind OpenResty) | Port (FLAVOR=dev) | Image |
 | - | - | - | - |
 | OpenResty  | / | 8080 | ghcr.io/buschlab/cbioroxy |
 | cBioPortal | / | 8081 | ghcr.io/buschlab/cbioportal |

compose.yml

@@ -1,3 +1,4 @@
 include:
- - ./compose/base.yml
- - ./compose/${FLAVOR:-care}.yml
+  - path:
+      - ./compose/base.yml
+      - ./compose/${FLAVOR:-care}.yml

compose/dev.yml

@@ -2,7 +2,7 @@ services:
   cbioportal:
     image: ghcr.io/buschlab/cbioportal:${RELEASE:-latest}
     build:
-      context: services/cbioportal
+      context: ./services/cbioportal
       platforms:
         - "linux/amd64"
         - "linux/arm64"