Initial commit: digital-patients pipeline (clean, no large files)

Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.

docker-compose.yml

@@ -0,0 +1,48 @@
+services:
+  borzoi:
+    build:
+      context: .
+      dockerfile: Dockerfile_borzoi
+    image: harbor.cluster.omic.ai/omic/digital-patients/borzoi:latest
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]
+  vcf2prot:
+    build:
+      context: .
+      dockerfile: Dockerfile_vcf2prot
+    image: harbor.cluster.omic.ai/omic/digital-patients/vcf2prot:latest
+  rna2protexpression:
+    build:
+      context: .
+      dockerfile: Dockerfile_rna2protexpression
+    image: harbor.cluster.omic.ai/omic/digital-patients/rna2protexpression:latest
+  corto:
+    build:
+      context: .
+      dockerfile: Dockerfile_corto
+    image: harbor.cluster.omic.ai/omic/digital-patients/corto:latest
+  ecotyper:
+    build:
+      context: .
+      dockerfile: Dockerfile_ecotyper
+    image: harbor.cluster.omic.ai/omic/digital-patients/ecotyper:latest
+  synthea:
+    build:
+      context: .
+      dockerfile: Dockerfile_synthea
+    image: harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf
+  vep:
+    build:
+      context: .
+      dockerfile: Dockerfile_vep
+    image: harbor.cluster.omic.ai/omic/digital-patients/vep:1.0.0
+    volumes:
+      - ./app_filter/sample:/sample
+      - /data/vep_data:/data
+
+# export IMAGE_NAME=synthea:cudf && docker tag $IMAGE_NAME harbor.cluster.omic.ai/omic/digital-patients/$IMAGE_NAME && retry_command.sh docker --config ~/.config/bugra push harbor.cluster.omic.ai/omic/digital-patients/$IMAGE_NAME