Add netcleave and noah containers. Fix MHCFlurry path on singularity

Author: chdominguez

.github/workflows/docker-build.yml

@@ -15,9 +15,9 @@ on:
 
 env:
   DOCKER_IMAGE: predig
+  NOAH_IMAGE: noah
+  NETCLEAVE_IMAGE: netcleave
   DOCKER_BASE_IMAGE: predig-base
-  DOCKER_HUB_REPO: ${{ secrets.DOCKER_HUB_USERNAME }}/predig
-  DOCKER_HUB_BASE_REPO: ${{ secrets.DOCKER_HUB_USERNAME }}/predig-base
 
 jobs:
   build-base:
@@ -51,8 +51,8 @@ jobs:
         file: Base.Dockerfile
         push: true
         tags: |
-          ${{ env.DOCKER_HUB_BASE_REPO }}:latest
-          ${{ env.DOCKER_HUB_BASE_REPO }}:${{ github.sha }}
+          ${{ secrets.DOCKER_HUB_USERNAME }}/${{ env.DOCKER_BASE_IMAGE }}:latest
+          ${{ secrets.DOCKER_HUB_USERNAME }}/${{ env.DOCKER_BASE_IMAGE }}:${{ github.sha }}
 
   build-test-push:
     runs-on: self-hosted
@@ -77,7 +77,23 @@ jobs:
         file: Dockerfile
         load: true
         tags: ${{ env.DOCKER_IMAGE }}:latest
+    
+    - name: Build NOAH image
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        file: NOAH.Dockerfile
+        load: true
+        tags: ${{ env.NOAH_IMAGE }}:latest
 
+    - name: Build NetCleave image
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        file: NetCleave.Dockerfile
+        load: true
+        tags: ${{ env.NETCLEAVE_IMAGE }}:latest
+        
     - name: Run tests
       run: |
         wget https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.fasta.gz -O uniprot_sprot.fasta.gz
@@ -99,5 +115,25 @@ jobs:
         file: Dockerfile
         push: true
         tags: |
-          ${{ env.DOCKER_HUB_REPO }}:latest
-          ${{ env.DOCKER_HUB_REPO }}:${{ github.sha }}
+          ${{ secrets.DOCKER_HUB_USERNAME }}/${{ env.DOCKER_IMAGE }}:latest
+          ${{ secrets.DOCKER_HUB_USERNAME }}/${{ env.DOCKER_IMAGE }}:${{ github.sha }}
+
+    - name: Push NetCleave to Docker Hub
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        file: NetCleave.Dockerfile
+        push: true
+        tags: |
+          ${{ secrets.DOCKER_HUB_USERNAME }}/${{ env.NETCLEAVE_IMAGE }}:latest
+          ${{ secrets.DOCKER_HUB_USERNAME }}/${{ env.NETCLEAVE_IMAGE }}:${{ github.sha }}
+
+    - name: Push NOAH to Docker Hub
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        file: NOAH.Dockerfile
+        push: true
+        tags: |
+          ${{ secrets.DOCKER_HUB_USERNAME }}/${{ env.NOAH_IMAGE }}:latest
+          ${{ secrets.DOCKER_HUB_USERNAME }}/${{ env.NOAH_IMAGE }}:${{ github.sha }}

Dockerfile

@@ -16,7 +16,7 @@ RUN micromamba create -n predig_env -f /tmp/predig_env.yml -y
 RUN echo "source /opt/conda/envs/predig_env/bin/activate" >> /etc/bash.bashrc
 
 # Download mhcflurry models
-RUN micromamba run -n predig_env mhcflurry-downloads fetch models_class1_presentation
+# RUN micromamba run -n predig_env mhcflurry-downloads fetch models_class1_presentation
 
 # Copy the immuno container
 COPY Immuno /Immuno

Immuno/mhc_models/10755300.stderr

@@ -0,0 +1,3 @@
++ echo 'Subsequent stderr output redirected to stdout'
+Subsequent stderr output redirected to stdout
++ exec

Immuno/mhc_models/10755300.stdout

@@ -0,0 +1,3 @@
++ echo 'Subsequent stderr output redirected to stdout'
+Subsequent stderr output redirected to stdout
++ exec

Immuno/mhc_models/10755342.stderr

@@ -0,0 +1,3 @@
++ echo 'Subsequent stderr output redirected to stdout'
+Subsequent stderr output redirected to stdout
++ exec

Immuno/mhc_models/10755342.stdout

@@ -0,0 +1,3 @@
++ echo 'Subsequent stderr output redirected to stdout'
+Subsequent stderr output redirected to stdout
++ exec