From 2d216f7784fb3b87d312be143cdaba51399ca46a Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 16:28:31 +0200
Subject: [PATCH 01/22] test 1

---
 .github/workflows/buildContainer.yaml | 158 +++++++++++++++++---------
 1 file changed, 106 insertions(+), 52 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 6112c90..f047057 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -3,85 +3,139 @@ name: docker
 on:
   push:
     branches:
-      - 'smaller_deblur'
+      - 'restructure_github_actions'
 
 jobs:
-  docker:
+  build_main:
     strategy:
       matrix:
-        plugin: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
-                 "nginx", "qiita", "plugin_collector"
-                ]
+        container: ["nginx", "qiita", "plugin_collector"]
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout repository
+      - name: Checkout tinqiita repo
         uses: actions/checkout@v4
 
-      - name: Login to DockerHub
-        uses: docker/login-action@v3
-        with:
-          registry: harbor.computational.bio.uni-giessen.de
-          username: ${{ vars.HARBOR_CB_USERNAME }}
-          password: ${{ secrets.HARBOR_CB_SECRET }}
-
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
-      - name: Read version from file
+      - name: Read image version from dockerfile
         id: vars
         run: |
-          VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+          VERSION=$(head -n 1 Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
           echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-          cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/trigger_noconda.py Images/trigger.py Images/nginx/nginx_qiita.conf Images/${{ matrix.plugin }}/requirements.txt .
+          cp Images/${{ matrix.container }}/start_${{ matrix.container }}.sh Images/test_plugin.sh Images/nginx/nginx_qiita.conf Images/${{ matrix.container }}/requirements.txt .
           cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
           cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
 
-      - name: Make tinqiita targets
+      - name: Create certificate and fake reference databases
         # second copy of "qiita_server_certificates" is necessary to match path for docker build, first copy for mounting into container
         run: |
-          make ./references/qiita_server_certificates ./references/qp-deblur/reference-gg-raxml-bl.tre ./references/qp-target-gene ./environments/qiita_db.env ./environments/qiita.env config
+          make ./references/qiita_server_certificates ./environments/qiita_db.env ./environments/qiita.env config
+          mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
+          for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
           cp -r ./references/qiita_server_certificates ./qiita_server_certificates
 
-      - name: Build Image (but do not push yet)
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build main qiita Images and push to github's own registry
         uses: docker/build-push-action@v6
         with:
           context: .
           push: false
           load: true
-          file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-          tags: tinqiita/${{ matrix.plugin }}:testcandidate
+          file: Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile
+          tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
+  
+#   build_plugins:
+#     needs: build_main
+#     strategy:
+#       matrix:
+#         container: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder"]
+#     runs-on: ubuntu-latest
+#     steps:
 
-      - name: debug docker
-        run: |
-          docker image ls -a
-          docker ps -a
+# jobs:
+#   docker:
+#     strategy:
+#       matrix:
+#         plugin: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
+#                  "nginx", "qiita", "plugin_collector"
+#                 ]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - name: Checkout repository
+#         uses: actions/checkout@v4
 
-      - name: adapt compose file to select specific plugin
-        run: |
-          sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
-          sed -i "s|image: janssenlab/${{ matrix.plugin }}:latest|image: tinqiita/${{ matrix.plugin }}:testcandidate|" compose_github.yaml
+#       - name: Login to DockerHub
+#         uses: docker/login-action@v3
+#         with:
+#           registry: harbor.computational.bio.uni-giessen.de
+#           username: ${{ vars.HARBOR_CB_USERNAME }}
+#           password: ${{ secrets.HARBOR_CB_SECRET }}
 
-      - name: Run docker compose
-        if: ${{ !contains('nginx,qiita,plugin_collector', matrix.plugin) }}
-        uses: hoverkraft-tech/compose-action@v2.0.1
-        with:
-          compose-file: "compose_github.yaml"
-          services: |
-            nginx
-      - name: Execute tests in the running services (wait till qiita plugins are registered)
-        if: ${{ !contains('nginx,qiita,plugin_collector', matrix.plugin) }}
-        run: |
-          sleep 5
-          docker compose exec qiita /bin/bash -c "cat /logs/*; cat /qiita_plugins/*"
-          docker compose exec ${{ matrix.plugin }} /bin/bash -c "PLUGIN=${{ matrix.plugin }} bash /test_plugin.sh"
+#       - name: Set up Docker Buildx
+#         uses: docker/setup-buildx-action@v3
 
-      - name: Push production image (only if tests passed)
-        if: success()
-        uses: docker/build-push-action@v6
-        with:
-          context: .
-          push: true
-          file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-          tags: |
-            harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.plugin }}:${{ env.IMAGE_TAG }}
-            harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.plugin }}:latest
+#       - name: Read version from file
+#         id: vars
+#         run: |
+#           VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+#           echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+#           cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/trigger_noconda.py Images/trigger.py Images/nginx/nginx_qiita.conf Images/${{ matrix.plugin }}/requirements.txt .
+#           cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
+#           cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
+
+#       - name: Make tinqiita targets
+#         # second copy of "qiita_server_certificates" is necessary to match path for docker build, first copy for mounting into container
+#         run: |
+#           make ./references/qiita_server_certificates ./references/qp-deblur/reference-gg-raxml-bl.tre ./references/qp-target-gene ./environments/qiita_db.env ./environments/qiita.env config
+#           cp -r ./references/qiita_server_certificates ./qiita_server_certificates
+
+#       - name: Build Image (but do not push yet)
+#         uses: docker/build-push-action@v6
+#         with:
+#           context: .
+#           push: false
+#           load: true
+#           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+#           tags: tinqiita/${{ matrix.plugin }}:testcandidate
+
+#       - name: debug docker
+#         run: |
+#           docker image ls -a
+#           docker ps -a
+
+#       - name: adapt compose file to select specific plugin
+#         run: |
+#           sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
+#           sed -i "s|image: janssenlab/${{ matrix.plugin }}:latest|image: tinqiita/${{ matrix.plugin }}:testcandidate|" compose_github.yaml
+
+#       - name: Run docker compose
+#         if: ${{ !contains('nginx,qiita,plugin_collector', matrix.plugin) }}
+#         uses: hoverkraft-tech/compose-action@v2.0.1
+#         with:
+#           compose-file: "compose_github.yaml"
+#           services: |
+#             nginx
+#       - name: Execute tests in the running services (wait till qiita plugins are registered)
+#         if: ${{ !contains('nginx,qiita,plugin_collector', matrix.plugin) }}
+#         run: |
+#           sleep 5
+#           docker compose exec qiita /bin/bash -c "cat /logs/*; cat /qiita_plugins/*"
+#           docker compose exec ${{ matrix.plugin }} /bin/bash -c "PLUGIN=${{ matrix.plugin }} bash /test_plugin.sh"
+
+#       - name: Push production image (only if tests passed)
+#         if: success()
+#         uses: docker/build-push-action@v6
+#         with:
+#           context: .
+#           push: true
+#           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+#           tags: |
+#             harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.plugin }}:${{ env.IMAGE_TAG }}
+#             harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.plugin }}:latest

From 6d94ac72b46619634a396584bc0c53800d3979fa Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 16:52:59 +0200
Subject: [PATCH 02/22] two phases

---
 .github/workflows/buildContainer.yaml | 63 ++++++++++++++++++++++-----
 compose_github.yaml                   | 10 ++---
 2 files changed, 57 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index f047057..04b6f44 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -27,12 +27,10 @@ jobs:
           cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
           cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
 
-      - name: Create certificate and fake reference databases
+      - name: Create certificate
         # second copy of "qiita_server_certificates" is necessary to match path for docker build, first copy for mounting into container
         run: |
           make ./references/qiita_server_certificates ./environments/qiita_db.env ./environments/qiita.env config
-          mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
-          for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
           cp -r ./references/qiita_server_certificates ./qiita_server_certificates
 
       - name: Log in to GitHub Container Registry
@@ -42,7 +40,7 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Build main qiita Images and push to github's own registry
+      - name: Build main qiita images and push to github's own registry
         uses: docker/build-push-action@v6
         with:
           context: .
@@ -51,13 +49,56 @@ jobs:
           file: Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile
           tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
   
-#   build_plugins:
-#     needs: build_main
-#     strategy:
-#       matrix:
-#         container: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder"]
-#     runs-on: ubuntu-latest
-#     steps:
+  build_plugins:
+    needs: build_main
+    strategy:
+      matrix:
+        plugin: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder"]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout tinqiita repo
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Read image version from dockerfile
+        id: vars
+        run: |
+          VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+          cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt .
+
+      - name: Create fake reference databases
+        run: |
+          mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
+          for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
+
+      - name: Build plugin images
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: false
+          load: true
+          file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+
+      - name: adapt compose file to select specific plugin
+        run: |
+          sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
+
+      - name: Run docker compose
+        uses: hoverkraft-tech/compose-action@v2.0.1
+        with:
+          compose-file: "compose_github.yaml"
+          services: |
+            nginx
+
+      - name: Execute tests in the running services
+        run: |
+          sleep 5
+          docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
+
+
 
 # jobs:
 #   docker:
diff --git a/compose_github.yaml b/compose_github.yaml
index ddb6791..0767e7b 100644
--- a/compose_github.yaml
+++ b/compose_github.yaml
@@ -27,7 +27,7 @@ services:
     #   start_period: 20s
 
   qiita-initialize-db:
-    image: harbor.computational.bio.uni-giessen.de/tinqiita/qiita:latest
+    image: ghcr.io/qiita-keycloak/qiita:testcandidate
     command: ['/start_qiita-initDB.sh']
     depends_on:
       - qiita-db
@@ -46,7 +46,7 @@ services:
       - qiita-net
 
   qiita:
-      image: harbor.computational.bio.uni-giessen.de/tinqiita/qiita:latest
+      image: ghcr.io/qiita-keycloak/qiita:testcandidate
       build: # image wird hier direkt gebaut
         context: ./Images/qiita
         dockerfile: Dockerfile
@@ -82,7 +82,7 @@ services:
       - "21174:21174"
 
   qiita-worker:
-      image: harbor.computational.bio.uni-giessen.de/tinqiita/qiita:latest
+      image: ghcr.io/qiita-keycloak/qiita:testcandidate
       build: # image wird hier direkt gebaut
         context: ./Images/qiita
         dockerfile: Dockerfile
@@ -142,7 +142,7 @@ services:
     #   start_period: 20s
 
   nginx:
-    image: harbor.computational.bio.uni-giessen.de/tinqiita/nginx:latest
+    image: ghcr.io/qiita-keycloak/nginx:testcandidate
     build:
       context: ./Images/nginx
       dockerfile: Dockerfile
@@ -306,7 +306,7 @@ services:
   plugin-collector:
     # 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: harbor.computational.bio.uni-giessen.de/tinqiita/plugin_collector:latest
+    image: ghcr.io/qiita-keycloak/plugin_collector:testcandidate
     restart: no
     networks:
       - qiita-net

From 6a6d81409ca38fa3515f62f3d08ff344bafe35ff Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 17:03:20 +0200
Subject: [PATCH 03/22] up/download certificates between jobs

---
 .github/workflows/buildContainer.yaml         | 25 ++++++++++++++++++-
 .../plugin_collector.dockerfile               |  2 +-
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 04b6f44..9720957 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -33,6 +33,12 @@ jobs:
           make ./references/qiita_server_certificates ./environments/qiita_db.env ./environments/qiita.env config
           cp -r ./references/qiita_server_certificates ./qiita_server_certificates
 
+      - name: Store certifactes for follow up jobs
+        uses: actions/upload-artifact@v4
+        with:
+          name: certificates
+          path: ./references/qiita_server_certificates ./qiita_server_certificates
+
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@v3
         with:
@@ -44,10 +50,11 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: .
-          push: false
           load: true
           file: Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile
           tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
+          cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+          cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
   
   build_plugins:
     needs: build_main
@@ -69,6 +76,11 @@ jobs:
           echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
           cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt .
 
+      - name: Download certificates from job build_main
+        uses: actions/download-artifact@v4
+        with:
+          name: certificates
+
       - name: Create fake reference databases
         run: |
           mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
@@ -98,6 +110,17 @@ jobs:
           sleep 5
           docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
 
+      - name: Push production image (only if tests passed)
+        if: success()
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+          tags: |
+            tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
+            cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+            cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
 
 
 # jobs:
diff --git a/Images/plugin_collector/plugin_collector.dockerfile b/Images/plugin_collector/plugin_collector.dockerfile
index 799da21..452c5b0 100644
--- a/Images/plugin_collector/plugin_collector.dockerfile
+++ b/Images/plugin_collector/plugin_collector.dockerfile
@@ -14,4 +14,4 @@ COPY fix_test_db.py /fix_test_db.py
 COPY start_plugin_collector.sh /start_plugin_collector.sh
 RUN chmod u+x /start_plugin_collector.sh
 
-CMD /start_plugin_collector.sh
\ No newline at end of file
+CMD ["/start_plugin_collector.sh"]

From 161c30644b1838b603a2f6a80039b98bdba609ea Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 17:04:46 +0200
Subject: [PATCH 04/22] login to ghcr

---
 .github/workflows/buildContainer.yaml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 9720957..e29aa12 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -86,6 +86,13 @@ jobs:
           mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
           for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
 
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Build plugin images
         uses: docker/build-push-action@v6
         with:

From d87b55e57d2a6e8b6851bab04227bc6fde11e107 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 17:09:45 +0200
Subject: [PATCH 05/22] adding phase3: publish images

---
 .github/workflows/buildContainer.yaml | 112 ++++++++------------------
 1 file changed, 32 insertions(+), 80 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index e29aa12..68f202d 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -129,84 +129,36 @@ jobs:
             cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
             cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
 
+  publish_images:
+    needs: build_plugins
+    strategy:
+      matrix:
+        images: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
+                 "nginx", "qiita", "plugin_collector"]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout tinqiita repo
+        uses: actions/checkout@v4
 
-# jobs:
-#   docker:
-#     strategy:
-#       matrix:
-#         plugin: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
-#                  "nginx", "qiita", "plugin_collector"
-#                 ]
-#     runs-on: ubuntu-latest
-#     steps:
-#       - name: Checkout repository
-#         uses: actions/checkout@v4
-
-#       - name: Login to DockerHub
-#         uses: docker/login-action@v3
-#         with:
-#           registry: harbor.computational.bio.uni-giessen.de
-#           username: ${{ vars.HARBOR_CB_USERNAME }}
-#           password: ${{ secrets.HARBOR_CB_SECRET }}
-
-#       - name: Set up Docker Buildx
-#         uses: docker/setup-buildx-action@v3
-
-#       - name: Read version from file
-#         id: vars
-#         run: |
-#           VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
-#           echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-#           cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/trigger_noconda.py Images/trigger.py Images/nginx/nginx_qiita.conf Images/${{ matrix.plugin }}/requirements.txt .
-#           cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
-#           cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
-
-#       - name: Make tinqiita targets
-#         # second copy of "qiita_server_certificates" is necessary to match path for docker build, first copy for mounting into container
-#         run: |
-#           make ./references/qiita_server_certificates ./references/qp-deblur/reference-gg-raxml-bl.tre ./references/qp-target-gene ./environments/qiita_db.env ./environments/qiita.env config
-#           cp -r ./references/qiita_server_certificates ./qiita_server_certificates
-
-#       - name: Build Image (but do not push yet)
-#         uses: docker/build-push-action@v6
-#         with:
-#           context: .
-#           push: false
-#           load: true
-#           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-#           tags: tinqiita/${{ matrix.plugin }}:testcandidate
-
-#       - name: debug docker
-#         run: |
-#           docker image ls -a
-#           docker ps -a
-
-#       - name: adapt compose file to select specific plugin
-#         run: |
-#           sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
-#           sed -i "s|image: janssenlab/${{ matrix.plugin }}:latest|image: tinqiita/${{ matrix.plugin }}:testcandidate|" compose_github.yaml
-
-#       - name: Run docker compose
-#         if: ${{ !contains('nginx,qiita,plugin_collector', matrix.plugin) }}
-#         uses: hoverkraft-tech/compose-action@v2.0.1
-#         with:
-#           compose-file: "compose_github.yaml"
-#           services: |
-#             nginx
-#       - name: Execute tests in the running services (wait till qiita plugins are registered)
-#         if: ${{ !contains('nginx,qiita,plugin_collector', matrix.plugin) }}
-#         run: |
-#           sleep 5
-#           docker compose exec qiita /bin/bash -c "cat /logs/*; cat /qiita_plugins/*"
-#           docker compose exec ${{ matrix.plugin }} /bin/bash -c "PLUGIN=${{ matrix.plugin }} bash /test_plugin.sh"
-
-#       - name: Push production image (only if tests passed)
-#         if: success()
-#         uses: docker/build-push-action@v6
-#         with:
-#           context: .
-#           push: true
-#           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-#           tags: |
-#             harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.plugin }}:${{ env.IMAGE_TAG }}
-#             harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.plugin }}:latest
+      - name: Login to computational.bio registry
+        uses: docker/login-action@v3
+        with:
+          registry: harbor.computational.bio.uni-giessen.de
+          username: ${{ vars.HARBOR_CB_USERNAME }}
+          password: ${{ secrets.HARBOR_CB_SECRET }}
+
+      - name: Read image version from dockerfile
+        id: vars
+        run: |
+          VERSION=$(head -n 1 Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+
+      - name: Push production image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          file: Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile
+          tags: |
+            harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:${{ env.IMAGE_TAG }}
+            harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:latest

From 504220c6caa8f89936701bf32e95f97f9fc2b119 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 17:15:20 +0200
Subject: [PATCH 06/22] transfer single dir

---
 .github/workflows/buildContainer.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 68f202d..d0b4d36 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -37,7 +37,7 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: certificates
-          path: ./references/qiita_server_certificates ./qiita_server_certificates
+          path: ./qiita_server_certificates
 
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@v3
@@ -80,9 +80,11 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: certificates
+          path: ./qiita_server_certificates
 
       - name: Create fake reference databases
         run: |
+          cp -r ./references/qiita_server_certificates ./qiita_server_certificates
           mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
           for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
 

From 8b3992c08f87761888a294751e4cad085f516af3 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 17:17:55 +0200
Subject: [PATCH 07/22] only store artefact in one of matrix jobs

---
 .github/workflows/buildContainer.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index d0b4d36..2353425 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -34,6 +34,7 @@ jobs:
           cp -r ./references/qiita_server_certificates ./qiita_server_certificates
 
       - name: Store certifactes for follow up jobs
+        if: ${{ matrix.container == 'nginx' }}
         uses: actions/upload-artifact@v4
         with:
           name: certificates

From 57d73ea7fb0bfc42e83fa6f5f0acb0bb2729cd9b Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 20:34:40 +0200
Subject: [PATCH 08/22] just certificates

---
 .github/workflows/buildContainer.yaml | 297 +++++++++++++-------------
 1 file changed, 154 insertions(+), 143 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 2353425..bbd3565 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -1,3 +1,5 @@
+# todo: "make" files once and push around through artifacts!
+
 name: docker
 
 on:
@@ -6,27 +8,12 @@ on:
       - 'restructure_github_actions'
 
 jobs:
-  build_main:
-    strategy:
-      matrix:
-        container: ["nginx", "qiita", "plugin_collector"]
+  make_certificates:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout tinqiita repo
         uses: actions/checkout@v4
 
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
-      - name: Read image version from dockerfile
-        id: vars
-        run: |
-          VERSION=$(head -n 1 Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
-          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-          cp Images/${{ matrix.container }}/start_${{ matrix.container }}.sh Images/test_plugin.sh Images/nginx/nginx_qiita.conf Images/${{ matrix.container }}/requirements.txt .
-          cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
-          cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
-
       - name: Create certificate
         # second copy of "qiita_server_certificates" is necessary to match path for docker build, first copy for mounting into container
         run: |
@@ -34,134 +21,158 @@ jobs:
           cp -r ./references/qiita_server_certificates ./qiita_server_certificates
 
       - name: Store certifactes for follow up jobs
-        if: ${{ matrix.container == 'nginx' }}
         uses: actions/upload-artifact@v4
         with:
           name: certificates
-          path: ./qiita_server_certificates
-
-      - name: Log in to GitHub Container Registry
-        uses: docker/login-action@v3
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Build main qiita images and push to github's own registry
-        uses: docker/build-push-action@v6
-        with:
-          context: .
-          load: true
-          file: Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile
-          tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
-          cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
-          cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
+          path: |
+            ./qiita_server_certificates
+            ./references/qiita_server_certificates
+
+  # build_main:
+  #   needs: make_certificates
+  #   strategy:
+  #     matrix:
+  #       container: ["nginx", "qiita", "plugin_collector"]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout tinqiita repo
+  #       uses: actions/checkout@v4
+
+  #     - name: Set up Docker Buildx
+  #       uses: docker/setup-buildx-action@v3
+
+  #     - name: Read image version from dockerfile
+  #       id: vars
+  #       run: |
+  #         VERSION=$(head -n 1 Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+  #         echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+  #         cp Images/${{ matrix.container }}/start_${{ matrix.container }}.sh Images/test_plugin.sh Images/nginx/nginx_qiita.conf Images/${{ matrix.container }}/requirements.txt .
+  #         cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
+  #         cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
+
+
+  #     - name: Log in to GitHub Container Registry
+  #       uses: docker/login-action@v3
+  #       with:
+  #         registry: ghcr.io
+  #         username: ${{ github.actor }}
+  #         password: ${{ secrets.GITHUB_TOKEN }}
+
+  #     - name: Build main qiita images and push to github's own registry
+  #       uses: docker/build-push-action@v6
+  #       with:
+  #         context: .
+  #         load: true
+  #         file: Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile
+  #         tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
+  #         cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+  #         cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
   
-  build_plugins:
-    needs: build_main
-    strategy:
-      matrix:
-        plugin: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder"]
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout tinqiita repo
-        uses: actions/checkout@v4
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
-      - name: Read image version from dockerfile
-        id: vars
-        run: |
-          VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
-          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-          cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt .
-
-      - name: Download certificates from job build_main
-        uses: actions/download-artifact@v4
-        with:
-          name: certificates
-          path: ./qiita_server_certificates
-
-      - name: Create fake reference databases
-        run: |
-          cp -r ./references/qiita_server_certificates ./qiita_server_certificates
-          mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
-          for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
-
-      - name: Log in to GitHub Container Registry
-        uses: docker/login-action@v3
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Build plugin images
-        uses: docker/build-push-action@v6
-        with:
-          context: .
-          push: false
-          load: true
-          file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-
-      - name: adapt compose file to select specific plugin
-        run: |
-          sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
-
-      - name: Run docker compose
-        uses: hoverkraft-tech/compose-action@v2.0.1
-        with:
-          compose-file: "compose_github.yaml"
-          services: |
-            nginx
-
-      - name: Execute tests in the running services
-        run: |
-          sleep 5
-          docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
-
-      - name: Push production image (only if tests passed)
-        if: success()
-        uses: docker/build-push-action@v6
-        with:
-          context: .
-          push: true
-          file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-          tags: |
-            tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
-            cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
-            cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
-
-  publish_images:
-    needs: build_plugins
-    strategy:
-      matrix:
-        images: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
-                 "nginx", "qiita", "plugin_collector"]
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout tinqiita repo
-        uses: actions/checkout@v4
-
-      - name: Login to computational.bio registry
-        uses: docker/login-action@v3
-        with:
-          registry: harbor.computational.bio.uni-giessen.de
-          username: ${{ vars.HARBOR_CB_USERNAME }}
-          password: ${{ secrets.HARBOR_CB_SECRET }}
-
-      - name: Read image version from dockerfile
-        id: vars
-        run: |
-          VERSION=$(head -n 1 Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
-          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-
-      - name: Push production image
-        uses: docker/build-push-action@v6
-        with:
-          context: .
-          push: true
-          file: Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile
-          tags: |
-            harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:${{ env.IMAGE_TAG }}
-            harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:latest
+  # build_plugins:
+  #   needs: build_main
+  #   strategy:
+  #     matrix:
+  #       plugin: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder"]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout tinqiita repo
+  #       uses: actions/checkout@v4
+
+  #     - name: Set up Docker Buildx
+  #       uses: docker/setup-buildx-action@v3
+
+  #     - name: Read image version from dockerfile
+  #       id: vars
+  #       run: |
+  #         VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+  #         echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+  #         cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt .
+
+  #     - name: Download certificates from job build_main
+  #       uses: actions/download-artifact@v4
+  #       with:
+  #         name: certificates
+  #         path: ./qiita_server_certificates
+
+  #     - name: Create fake reference databases
+  #       run: |
+  #         cp -r ./references/qiita_server_certificates ./qiita_server_certificates
+  #         mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
+  #         for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
+
+  #     - name: Log in to GitHub Container Registry
+  #       uses: docker/login-action@v3
+  #       with:
+  #         registry: ghcr.io
+  #         username: ${{ github.actor }}
+  #         password: ${{ secrets.GITHUB_TOKEN }}
+
+  #     - name: Build plugin images
+  #       uses: docker/build-push-action@v6
+  #       with:
+  #         context: .
+  #         push: false
+  #         load: true
+  #         file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+
+  #     - name: adapt compose file to select specific plugin
+  #       run: |
+  #         sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
+
+  #     - name: Run docker compose
+  #       uses: hoverkraft-tech/compose-action@v2.0.1
+  #       with:
+  #         compose-file: "compose_github.yaml"
+  #         services: |
+  #           nginx
+
+  #     - name: Execute tests in the running services
+  #       run: |
+  #         sleep 5
+  #         docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
+
+  #     - name: Push production image (only if tests passed)
+  #       if: success()
+  #       uses: docker/build-push-action@v6
+  #       with:
+  #         context: .
+  #         push: true
+  #         file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+  #         tags: |
+  #           tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
+  #           cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+  #           cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
+
+  # publish_images:
+  #   needs: build_plugins
+  #   strategy:
+  #     matrix:
+  #       images: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
+  #                "nginx", "qiita", "plugin_collector"]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout tinqiita repo
+  #       uses: actions/checkout@v4
+
+  #     - name: Login to computational.bio registry
+  #       uses: docker/login-action@v3
+  #       with:
+  #         registry: harbor.computational.bio.uni-giessen.de
+  #         username: ${{ vars.HARBOR_CB_USERNAME }}
+  #         password: ${{ secrets.HARBOR_CB_SECRET }}
+
+  #     - name: Read image version from dockerfile
+  #       id: vars
+  #       run: |
+  #         VERSION=$(head -n 1 Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+  #         echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+
+  #     - name: Push production image
+  #       uses: docker/build-push-action@v6
+  #       with:
+  #         context: .
+  #         push: true
+  #         file: Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile
+  #         tags: |
+  #           harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:${{ env.IMAGE_TAG }}
+  #           harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:latest

From dec95fa2ad84c4801bef1b703a1a53272d0f1109 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 20:37:51 +0200
Subject: [PATCH 09/22] now add build main image phase

---
 .github/workflows/buildContainer.yaml | 75 ++++++++++++++-------------
 1 file changed, 40 insertions(+), 35 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index bbd3565..c958107 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -28,45 +28,50 @@ jobs:
             ./qiita_server_certificates
             ./references/qiita_server_certificates
 
-  # build_main:
-  #   needs: make_certificates
-  #   strategy:
-  #     matrix:
-  #       container: ["nginx", "qiita", "plugin_collector"]
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Checkout tinqiita repo
-  #       uses: actions/checkout@v4
-
-  #     - name: Set up Docker Buildx
-  #       uses: docker/setup-buildx-action@v3
+  build_main:
+    needs: make_certificates
+    strategy:
+      matrix:
+        container: ["nginx", "qiita", "plugin_collector"]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout tinqiita repo
+        uses: actions/checkout@v4
 
-  #     - name: Read image version from dockerfile
-  #       id: vars
-  #       run: |
-  #         VERSION=$(head -n 1 Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
-  #         echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-  #         cp Images/${{ matrix.container }}/start_${{ matrix.container }}.sh Images/test_plugin.sh Images/nginx/nginx_qiita.conf Images/${{ matrix.container }}/requirements.txt .
-  #         cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
-  #         cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
 
+      - name: Read image version from dockerfile
+        id: vars
+        run: |
+          VERSION=$(head -n 1 Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+          cp Images/${{ matrix.container }}/start_${{ matrix.container }}.sh Images/test_plugin.sh Images/nginx/nginx_qiita.conf Images/${{ matrix.container }}/requirements.txt .
+          cp Images/qiita/config_portal.cfg Images/qiita/config_qiita_oidc.cfg Images/qiita/drop_workflows.py Images/qiita/start_plugin.py Images/qiita/start_qiita-initDB.sh Images/qiita/start_qiita.sh .
+          cp Images/plugin_collector/collect_configs.py Images/plugin_collector/fix_test_db.py Images/plugin_collector/stefan_cert.conf Images/plugin_collector/stefan_csr.conf .
+
+      - name: Download certificates from job build_main
+        uses: actions/download-artifact@v4
+        with:
+          name: certificates
+          path: ./          
 
-  #     - name: Log in to GitHub Container Registry
-  #       uses: docker/login-action@v3
-  #       with:
-  #         registry: ghcr.io
-  #         username: ${{ github.actor }}
-  #         password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
-  #     - name: Build main qiita images and push to github's own registry
-  #       uses: docker/build-push-action@v6
-  #       with:
-  #         context: .
-  #         load: true
-  #         file: Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile
-  #         tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
-  #         cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
-  #         cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
+      - name: Build main qiita images and push to github's own registry
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          load: true
+          file: Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile
+          tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
+          cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+          cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
   
   # build_plugins:
   #   needs: build_main

From 85e394b02afb25a63de571aff3b9be6bbca2e732 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 20:47:21 +0200
Subject: [PATCH 10/22] add plugin build

---
 .github/workflows/buildContainer.yaml | 151 +++++++++++++++-----------
 1 file changed, 86 insertions(+), 65 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index c958107..0c796ee 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -72,81 +72,102 @@ jobs:
           tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
           cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
           cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
-  
-  # build_plugins:
-  #   needs: build_main
-  #   strategy:
-  #     matrix:
-  #       plugin: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder"]
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Checkout tinqiita repo
-  #       uses: actions/checkout@v4
 
-  #     - name: Set up Docker Buildx
-  #       uses: docker/setup-buildx-action@v3
+  make_references:
+    needs: build_main
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout tinqiita repo
+        uses: actions/checkout@v4
 
-  #     - name: Read image version from dockerfile
-  #       id: vars
-  #       run: |
-  #         VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
-  #         echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-  #         cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt .
+      - name: Create fake reference databases
+        run: |
+          mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
+          for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
 
-  #     - name: Download certificates from job build_main
-  #       uses: actions/download-artifact@v4
-  #       with:
-  #         name: certificates
-  #         path: ./qiita_server_certificates
+      - name: Store fake references for follow up jobs
+        uses: actions/upload-artifact@v4
+        with:
+          name: fake_references
+          path: |
+            ./references/qp-deblur
+            ./references/qp-target-gene
 
-  #     - name: Create fake reference databases
-  #       run: |
-  #         cp -r ./references/qiita_server_certificates ./qiita_server_certificates
-  #         mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
-  #         for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
+  build_plugins:
+    needs:
+      - build_main
+      - make_references
+    strategy:
+      matrix:
+        plugin: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder"]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout tinqiita repo
+        uses: actions/checkout@v4
 
-  #     - name: Log in to GitHub Container Registry
-  #       uses: docker/login-action@v3
-  #       with:
-  #         registry: ghcr.io
-  #         username: ${{ github.actor }}
-  #         password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
 
-  #     - name: Build plugin images
-  #       uses: docker/build-push-action@v6
-  #       with:
-  #         context: .
-  #         push: false
-  #         load: true
-  #         file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+      - name: Read image version from dockerfile
+        id: vars
+        run: |
+          VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+          cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt .
 
-  #     - name: adapt compose file to select specific plugin
-  #       run: |
-  #         sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
+      - name: Download certificates from job build_main
+        uses: actions/download-artifact@v4
+        with:
+          name: certificates
+          path: ./
+      - name: Download fake references
+        uses: actions/download-artifact@v4
+        with:
+          name: fake_references
+          path: ./
 
-  #     - name: Run docker compose
-  #       uses: hoverkraft-tech/compose-action@v2.0.1
-  #       with:
-  #         compose-file: "compose_github.yaml"
-  #         services: |
-  #           nginx
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
-  #     - name: Execute tests in the running services
-  #       run: |
-  #         sleep 5
-  #         docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
+      - name: Build plugin images
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: false
+          load: true
+          file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
 
-  #     - name: Push production image (only if tests passed)
-  #       if: success()
-  #       uses: docker/build-push-action@v6
-  #       with:
-  #         context: .
-  #         push: true
-  #         file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-  #         tags: |
-  #           tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
-  #           cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
-  #           cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
+      - name: adapt compose file to select specific plugin
+        run: |
+          sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
+
+      - name: Run docker compose
+        uses: hoverkraft-tech/compose-action@v2.0.1
+        with:
+          compose-file: "compose_github.yaml"
+          services: |
+            nginx
+
+      - name: Execute tests in the running services
+        run: |
+          sleep 5
+          docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
+
+      - name: Push production image (only if tests passed)
+        if: success()
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+          tags: |
+            tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
+            cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+            cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
 
   # publish_images:
   #   needs: build_plugins

From d70700690a57e12daf0eae888a01a7cc66dcc4b4 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 20:59:02 +0200
Subject: [PATCH 11/22] copy missing files

---
 .github/workflows/buildContainer.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 0c796ee..f296909 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -113,7 +113,7 @@ jobs:
         run: |
           VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
           echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-          cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt .
+          cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt Images/trigger_noconda.py Images/trigger.py .
 
       - name: Download certificates from job build_main
         uses: actions/download-artifact@v4

From 96784464550e0b989a09d2c27b2cb0029adfcf4d Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 21:05:34 +0200
Subject: [PATCH 12/22] add env configuration files

---
 .github/workflows/buildContainer.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index f296909..510eca3 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -82,6 +82,7 @@ jobs:
 
       - name: Create fake reference databases
         run: |
+          make ./environments/qiita_db.env ./environments/qiita.env config
           mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
           for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
 
@@ -92,6 +93,7 @@ jobs:
           path: |
             ./references/qp-deblur
             ./references/qp-target-gene
+            ./environments
 
   build_plugins:
     needs:

From 33bb56621866a71a4b4781203d25175cb7286875 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 21:17:38 +0200
Subject: [PATCH 13/22] pull from ghcr

---
 compose_github.yaml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/compose_github.yaml b/compose_github.yaml
index 0767e7b..b2dde1e 100644
--- a/compose_github.yaml
+++ b/compose_github.yaml
@@ -170,7 +170,7 @@ services:
     #   start_period: 10s
 
   qtp-biom:
-    image: tinqiita/qtp-biom:testcandidate
+    image: ghcr.io/qiita-keycloak/qtp-biom:testcandidate
     command: ['./start_qtp-biom.sh']
     # network_mode: host
     # stdin_open: true
@@ -186,7 +186,7 @@ services:
       - qiita-net
 
   qtp-sequencing:
-    image: tinqiita/qtp-sequencing:testcandidate
+    image: ghcr.io/qiita-keycloak/qtp-sequencing:testcandidate
     command: ['./start_qtp-sequencing.sh']
     # network_mode: host
     # stdin_open: true
@@ -208,7 +208,7 @@ services:
     #   start_period: 3s
 
   qp-target-gene:
-    image: tinqiita/qp-target-gene:testcandidate
+    image: ghcr.io/qiita-keycloak/qp-target-gene:testcandidate
     command: ['./start_qp-target-gene.sh']
     # network_mode: host
     # stdin_open: true
@@ -225,7 +225,7 @@ services:
       - qiita-net
 
   qtp-visualization:
-    image: tinqiita/qtp-visualization:testcandidate
+    image: ghcr.io/qiita-keycloak/qtp-visualization:testcandidate
     command: ['./start_qtp-visualization.sh']
     # network_mode: host
     # stdin_open: true
@@ -241,7 +241,7 @@ services:
       - qiita-net
 
   qtp-diversity:
-    image: tinqiita/qtp-diversity:testcandidate
+    image: ghcr.io/qiita-keycloak/qtp-diversity:testcandidate
     command: ['./start_qtp-diversity.sh']
     # network_mode: host
     # stdin_open: true
@@ -257,7 +257,7 @@ services:
       - qiita-net
 
   qp-deblur:
-    image: tinqiita/qp-deblur:testcandidate
+    image: ghcr.io/qiita-keycloak/qp-deblur:testcandidate
     command: ['./start_qp-deblur.sh']
     restart: no
     volumes:
@@ -271,7 +271,7 @@ services:
       - qiita-net
 
   qp-qiime2:
-    image: tinqiita/qp-qiime2:testcandidate
+    image: ghcr.io/qiita-keycloak/qp-qiime2:testcandidate
     command: ['./start_qp-qiime2.sh']
     # network_mode: host
     # stdin_open: true
@@ -288,7 +288,7 @@ services:
       - qiita-net
 
   qtp-job-output-folder:
-    image: tinqiita/qtp-job-output-folder:testcandidate
+    image: ghcr.io/qiita-keycloak/qtp-job-output-folder:testcandidate
     command: ['./start_qtp-job-output-folder.sh']
     # network_mode: host
     # stdin_open: true

From d672d22f159fe39c1072c0c6fec23de0f67504f8 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 21:33:49 +0200
Subject: [PATCH 14/22] push to ghcr

---
 .github/workflows/buildContainer.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 510eca3..753ccc1 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -139,9 +139,11 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: .
-          push: false
           load: true
           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+          tags: tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
+          cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+          cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
 
       - name: adapt compose file to select specific plugin
         run: |

From 8233831ffe0d34789e94057b8679b0ceef265dd3 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 21:34:29 +0200
Subject: [PATCH 15/22] fix yaml

---
 .github/workflows/buildContainer.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 753ccc1..8e9616a 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -141,7 +141,7 @@ jobs:
           context: .
           load: true
           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-          tags: tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
+          tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
           cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
           cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
 

From 0bdeb4d93925296e66a6c44c00732eeed1791bb7 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 21:49:28 +0200
Subject: [PATCH 16/22] adding jlab/

---
 compose_github.yaml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/compose_github.yaml b/compose_github.yaml
index b2dde1e..443a6f9 100644
--- a/compose_github.yaml
+++ b/compose_github.yaml
@@ -27,7 +27,7 @@ services:
     #   start_period: 20s
 
   qiita-initialize-db:
-    image: ghcr.io/qiita-keycloak/qiita:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qiita:testcandidate
     command: ['/start_qiita-initDB.sh']
     depends_on:
       - qiita-db
@@ -46,7 +46,7 @@ services:
       - qiita-net
 
   qiita:
-      image: ghcr.io/qiita-keycloak/qiita:testcandidate
+      image: ghcr.io/jlab/qiita-keycloak/qiita:testcandidate
       build: # image wird hier direkt gebaut
         context: ./Images/qiita
         dockerfile: Dockerfile
@@ -82,7 +82,7 @@ services:
       - "21174:21174"
 
   qiita-worker:
-      image: ghcr.io/qiita-keycloak/qiita:testcandidate
+      image: ghcr.io/jlab/qiita-keycloak/qiita:testcandidate
       build: # image wird hier direkt gebaut
         context: ./Images/qiita
         dockerfile: Dockerfile
@@ -142,7 +142,7 @@ services:
     #   start_period: 20s
 
   nginx:
-    image: ghcr.io/qiita-keycloak/nginx:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/nginx:testcandidate
     build:
       context: ./Images/nginx
       dockerfile: Dockerfile
@@ -170,7 +170,7 @@ services:
     #   start_period: 10s
 
   qtp-biom:
-    image: ghcr.io/qiita-keycloak/qtp-biom:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qtp-biom:testcandidate
     command: ['./start_qtp-biom.sh']
     # network_mode: host
     # stdin_open: true
@@ -186,7 +186,7 @@ services:
       - qiita-net
 
   qtp-sequencing:
-    image: ghcr.io/qiita-keycloak/qtp-sequencing:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qtp-sequencing:testcandidate
     command: ['./start_qtp-sequencing.sh']
     # network_mode: host
     # stdin_open: true
@@ -208,7 +208,7 @@ services:
     #   start_period: 3s
 
   qp-target-gene:
-    image: ghcr.io/qiita-keycloak/qp-target-gene:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qp-target-gene:testcandidate
     command: ['./start_qp-target-gene.sh']
     # network_mode: host
     # stdin_open: true
@@ -225,7 +225,7 @@ services:
       - qiita-net
 
   qtp-visualization:
-    image: ghcr.io/qiita-keycloak/qtp-visualization:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qtp-visualization:testcandidate
     command: ['./start_qtp-visualization.sh']
     # network_mode: host
     # stdin_open: true
@@ -241,7 +241,7 @@ services:
       - qiita-net
 
   qtp-diversity:
-    image: ghcr.io/qiita-keycloak/qtp-diversity:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qtp-diversity:testcandidate
     command: ['./start_qtp-diversity.sh']
     # network_mode: host
     # stdin_open: true
@@ -257,7 +257,7 @@ services:
       - qiita-net
 
   qp-deblur:
-    image: ghcr.io/qiita-keycloak/qp-deblur:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qp-deblur:testcandidate
     command: ['./start_qp-deblur.sh']
     restart: no
     volumes:
@@ -271,7 +271,7 @@ services:
       - qiita-net
 
   qp-qiime2:
-    image: ghcr.io/qiita-keycloak/qp-qiime2:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qp-qiime2:testcandidate
     command: ['./start_qp-qiime2.sh']
     # network_mode: host
     # stdin_open: true
@@ -288,7 +288,7 @@ services:
       - qiita-net
 
   qtp-job-output-folder:
-    image: ghcr.io/qiita-keycloak/qtp-job-output-folder:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/qtp-job-output-folder:testcandidate
     command: ['./start_qtp-job-output-folder.sh']
     # network_mode: host
     # stdin_open: true
@@ -306,7 +306,7 @@ services:
   plugin-collector:
     # 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/qiita-keycloak/plugin_collector:testcandidate
+    image: ghcr.io/jlab/qiita-keycloak/plugin_collector:testcandidate
     restart: no
     networks:
       - qiita-net

From 2921b2f462bb84fe91d87b96e78086065f5aac85 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 22:04:08 +0200
Subject: [PATCH 17/22] push to ghcr

---
 .github/workflows/buildContainer.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 8e9616a..7158435 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -67,7 +67,7 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: .
-          load: true
+          push: true
           file: Images/${{ matrix.container }}/${{ matrix.container }}.dockerfile
           tags: ghcr.io/${{ github.repository }}/${{ matrix.container }}:testcandidate
           cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}

From d1a1b038c974ca4bba422818307e5a5ea7cca3fa Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 22:18:20 +0200
Subject: [PATCH 18/22] fix tag syntax

---
 .github/workflows/buildContainer.yaml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 7158435..55e54a9 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -168,10 +168,7 @@ jobs:
           context: .
           push: true
           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
-          tags: |
-            tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
-            cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
-            cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
+          tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
 
   # publish_images:
   #   needs: build_plugins

From d346019991ea321eeeb8da656be83ffa63f86474 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 11 Sep 2025 23:07:50 +0200
Subject: [PATCH 19/22] create real SEPP references for qp-deblur & push to
 habor

---
 .github/workflows/buildContainer.yaml | 83 +++++++++++++++------------
 1 file changed, 46 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 55e54a9..cdaefc2 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -80,11 +80,11 @@ jobs:
       - name: Checkout tinqiita repo
         uses: actions/checkout@v4
 
-      - name: Create fake reference databases
+      - name: Create partially fake reference databases
         run: |
-          make ./environments/qiita_db.env ./environments/qiita.env config
           mkdir -p ./references/qp-deblur/ ./references/qp-target-gene
-          for f in `echo "./references/qp-deblur/reference-gg-raxml-bl.tre references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
+          make ./environments/qiita_db.env ./environments/qiita.env config ./references/qp-deblur/reference-gg-raxml-bl.tre
+          for f in `echo "references/qp-target-gene/97_otus.fasta references/qp-target-gene/97_otus.tree references/qp-target-gene/97_otu_taxonomy.txt"`; do echo "fake" > $f; done
 
       - name: Store fake references for follow up jobs
         uses: actions/upload-artifact@v4
@@ -161,7 +161,7 @@ jobs:
           sleep 5
           docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
 
-      - name: Push production image (only if tests passed)
+      - name: Push image to ghcr (only if tests passed)
         if: success()
         uses: docker/build-push-action@v6
         with:
@@ -170,36 +170,45 @@ jobs:
           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
           tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
 
-  # publish_images:
-  #   needs: build_plugins
-  #   strategy:
-  #     matrix:
-  #       images: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
-  #                "nginx", "qiita", "plugin_collector"]
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Checkout tinqiita repo
-  #       uses: actions/checkout@v4
-
-  #     - name: Login to computational.bio registry
-  #       uses: docker/login-action@v3
-  #       with:
-  #         registry: harbor.computational.bio.uni-giessen.de
-  #         username: ${{ vars.HARBOR_CB_USERNAME }}
-  #         password: ${{ secrets.HARBOR_CB_SECRET }}
-
-  #     - name: Read image version from dockerfile
-  #       id: vars
-  #       run: |
-  #         VERSION=$(head -n 1 Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
-  #         echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
-
-  #     - name: Push production image
-  #       uses: docker/build-push-action@v6
-  #       with:
-  #         context: .
-  #         push: true
-  #         file: Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile
-  #         tags: |
-  #           harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:${{ env.IMAGE_TAG }}
-  #           harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:latest
+  publish_images:
+    needs:
+      - build_plugins
+      - build_main
+    strategy:
+      matrix:
+        images: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
+                 "nginx", "qiita", "plugin_collector"]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Login to computational.bio registry
+        uses: docker/login-action@v3
+        with:
+          registry: harbor.computational.bio.uni-giessen.de
+          username: ${{ vars.HARBOR_CB_USERNAME }}
+          password: ${{ secrets.HARBOR_CB_SECRET }}
+
+      - name: Pull image from GHCR
+        run: docker pull ghcr.io/${{ github.repository }}/{{ matrix.images }}:testcandidate
+
+      - name: Read image version from dockerfile
+        id: vars
+        run: |
+          VERSION=$(head -n 1 Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+          echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+
+      - name: Retag image for Docker Hub
+        run: docker tag \
+          ghcr.io/${{ github.repository }}/${{ matrix.images }}:testcandidate \
+          harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:${{ env.IMAGE_TAG }}
+
+      - name: Push image to Docker Hub
+        run: |
+          docker push harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:${{ env.IMAGE_TAG }}
+          docker push harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:latest

From 9ad6f15148edbbc8eadd6ee13dccafd3354c24f0 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 12 Sep 2025 07:29:30 +0200
Subject: [PATCH 20/22] make it a variable

---
 .github/workflows/buildContainer.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index cdaefc2..aec9d62 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -195,7 +195,7 @@ jobs:
           password: ${{ secrets.HARBOR_CB_SECRET }}
 
       - name: Pull image from GHCR
-        run: docker pull ghcr.io/${{ github.repository }}/{{ matrix.images }}:testcandidate
+        run: docker pull ghcr.io/${{ github.repository }}/${{ matrix.images }}:testcandidate
 
       - name: Read image version from dockerfile
         id: vars

From 702e85f220114b839a76cc4f426047f7d4fca87a Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 12 Sep 2025 08:39:58 +0200
Subject: [PATCH 21/22] checkout repo to obtain version number from docker file

---
 .github/workflows/buildContainer.yaml | 93 ++++++++++++++++++++++++---
 Images/qp-qiime2/qp-qiime2.dockerfile |  2 +
 2 files changed, 87 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index aec9d62..19bcc2c 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -170,16 +170,94 @@ jobs:
           file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
           tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
 
+  # build_mulit_plugins:
+  #   needs:
+  #     - build_plugins
+  #   strategy:
+  #     matrix:
+  #       plugin: ["qp-qiime2"]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout tinqiita repo
+  #       uses: actions/checkout@v4
+
+  #     - name: Set up Docker Buildx
+  #       uses: docker/setup-buildx-action@v3
+
+  #     - name: Read image version from dockerfile
+  #       id: vars
+  #       run: |
+  #         VERSION=$(head -n 1 Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+  #         echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
+  #         cp Images/${{ matrix.plugin }}/start_${{ matrix.plugin }}.sh Images/test_plugin.sh Images/${{ matrix.plugin }}/requirements.txt Images/trigger_noconda.py Images/trigger.py .
+
+  #     - name: Download certificates from job build_main
+  #       uses: actions/download-artifact@v4
+  #       with:
+  #         name: certificates
+  #         path: ./
+  #     - name: Download fake references
+  #       uses: actions/download-artifact@v4
+  #       with:
+  #         name: fake_references
+  #         path: ./
+
+  #     - name: Log in to GitHub Container Registry
+  #       uses: docker/login-action@v3
+  #       with:
+  #         registry: ghcr.io
+  #         username: ${{ github.actor }}
+  #         password: ${{ secrets.GITHUB_TOKEN }}
+
+  #     - name: Build plugin images
+  #       uses: docker/build-push-action@v6
+  #       with:
+  #         context: .
+  #         load: true
+  #         file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+  #         tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
+  #         cache-from: type=gha,scope=tinqiita-${{ github.ref_name }}
+  #         cache-to: type=gha,scope=tinqiita-${{ github.ref_name }},mode=max
+
+  #     - name: adapt compose file to select specific plugin
+  #       run: |
+  #         sed -i "s|||" compose_github.yaml
+  #         sed -i "s/MATRIXPLUGIN/${{ matrix.plugin }}/g" compose_github.yaml
+
+  #     - name: Run docker compose
+  #       uses: hoverkraft-tech/compose-action@v2.0.1
+  #       with:
+  #         compose-file: "compose_github.yaml"
+  #         services: |
+  #           nginx
+
+  #     - name: Execute tests in the running services
+  #       run: |
+  #         sleep 5
+  #         docker compose exec ${{ matrix.plugin }} /bin/bash -c "bash /test_plugin.sh"
+
+  #     - name: Push image to ghcr (only if tests passed)
+  #       if: success()
+  #       uses: docker/build-push-action@v6
+  #       with:
+  #         context: .
+  #         push: true
+  #         file: Images/${{ matrix.plugin }}/${{ matrix.plugin }}.dockerfile
+  #         tags: ghcr.io/${{ github.repository }}/${{ matrix.plugin }}:testcandidate
+
   publish_images:
     needs:
       - build_plugins
       - build_main
     strategy:
       matrix:
-        images: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
+        image: ["qp-deblur", "qtp-biom", "qtp-sequencing", "qtp-visualization", "qtp-diversity", "qp-target-gene", "qtp-job-output-folder",
                  "nginx", "qiita", "plugin_collector"]
     runs-on: ubuntu-latest
     steps:
+      - name: Checkout tinqiita repo
+        uses: actions/checkout@v4
+
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@v3
         with:
@@ -195,20 +273,19 @@ jobs:
           password: ${{ secrets.HARBOR_CB_SECRET }}
 
       - name: Pull image from GHCR
-        run: docker pull ghcr.io/${{ github.repository }}/${{ matrix.images }}:testcandidate
+        run: docker pull ghcr.io/${{ github.repository }}/${{ matrix.image }}:testcandidate
 
       - name: Read image version from dockerfile
         id: vars
         run: |
-          VERSION=$(head -n 1 Images/${{ matrix.images }}/${{ matrix.images }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
+          VERSION=$(head -n 1 Images/${{ matrix.image }}/${{ matrix.image }}.dockerfile | cut -d ":" -f 2- | tr -d " ")
           echo "IMAGE_TAG=$VERSION" >> $GITHUB_ENV
 
       - name: Retag image for Docker Hub
-        run: docker tag \
-          ghcr.io/${{ github.repository }}/${{ matrix.images }}:testcandidate \
-          harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:${{ env.IMAGE_TAG }}
+        run: |
+          docker tag ghcr.io/${{ github.repository }}/${{ matrix.image }}:testcandidate harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.image }}:${{ env.IMAGE_TAG }}
 
       - name: Push image to Docker Hub
         run: |
-          docker push harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:${{ env.IMAGE_TAG }}
-          docker push harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.images }}:latest
+          docker push harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.image }}:${{ env.IMAGE_TAG }}
+          docker push harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.image }}:latest
diff --git a/Images/qp-qiime2/qp-qiime2.dockerfile b/Images/qp-qiime2/qp-qiime2.dockerfile
index 6f63281..0cc7639 100644
--- a/Images/qp-qiime2/qp-qiime2.dockerfile
+++ b/Images/qp-qiime2/qp-qiime2.dockerfile
@@ -1,3 +1,5 @@
+# VERSION: 2025.09.12
+
 FROM ubuntu:24.04
 
 ARG MINIFORGE_VERSION=24.1.2-0

From 6a7f4c3cb50224035af2a9294c5bc76e3fbcf7c1 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Fri, 12 Sep 2025 10:47:57 +0200
Subject: [PATCH 22/22] also create local "latest" tag before pushing

---
 .github/workflows/buildContainer.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/buildContainer.yaml b/.github/workflows/buildContainer.yaml
index 19bcc2c..7f7c79b 100644
--- a/.github/workflows/buildContainer.yaml
+++ b/.github/workflows/buildContainer.yaml
@@ -284,6 +284,7 @@ jobs:
       - name: Retag image for Docker Hub
         run: |
           docker tag ghcr.io/${{ github.repository }}/${{ matrix.image }}:testcandidate harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.image }}:${{ env.IMAGE_TAG }}
+          docker tag ghcr.io/${{ github.repository }}/${{ matrix.image }}:testcandidate harbor.computational.bio.uni-giessen.de/tinqiita/${{ matrix.image }}:latest
 
       - name: Push image to Docker Hub
         run: |