use Kaniko instead of Docker in Docker

.gitlab-ci.yml

@@ -3,18 +3,14 @@ stages:
  
 build-alphafold:
   stage: build
-  image: docker:19.03
-  services:
-  - name: docker:19.03-dind
-    entrypoint: ["dockerd-entrypoint.sh"]
-    command: ["--mtu", "1450"]
-  variables:
-    IMAGE_TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_REF_SLUG
-    DOCKER_HOST: tcp://docker:2375
-    DOCKER_TLS_CERTDIR: ""
+  image:
+    name: gcr.io/kaniko-project/executor:debug
+    entrypoint: [""]
   script:
-    - docker info
-    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-    - docker build --pull -t $IMAGE_TAG -f docker/Dockerfile .
-    - docker push $IMAGE_TAG
-    
+    - mkdir -p /kaniko/.docker
+    - echo "{\"auths\":{\"$CI_REGISTRY\":{\"auth\":\"$(echo -n ${CI_REGISTRY_USER}:${CI_REGISTRY_PASSWORD} | base64)\"}}}" > /kaniko/.docker/config.json
+    - >
+      /kaniko/executor 
+      --context $CI_PROJECT_DIR
+      --dockerfile $CI_PROJECT_DIR/docker/Dockerfile 
+      --destination $CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA

docker/Dockerfile

@@ -37,7 +37,7 @@ RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh
     && mkdir /tmp/hh-suite/build
 WORKDIR /tmp/hh-suite/build
 RUN cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
-    && make -d && make install \
+    && make -j 4 && make install \
     && ln -s /opt/hhsuite/bin/* /usr/bin \
     && rm -rf /tmp/hh-suite