feat: Update vep version (#1567)

### Changed

- Update to latest VEP version
- Updated rank model to use gnomad_popmax since gnomAD_AF is no longer in use in the latest VEP version

### Fixed

- Fixed varcall_py27 container

Author: fevac

BALSAMIC/constants/cache.py

@@ -154,10 +154,10 @@ class DockerContainers(StrEnum):
             "dir_name": "genome",
         },
         "rank_score": {
-            "url": "https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/cancer/rank_model/cancer_rank_model_-v0.1-.ini",
+            "url": "https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/cancer/rank_model/cancer_rank_model_-v0.2-.ini",
             "file_type": FileType.TXT,
             "gzip": False,
-            "file_name": "cancer_rank_model_-v0.1-.ini",
+            "file_name": "cancer_rank_model_-v0.2-.ini",
             "dir_name": "genome",
         },
         "access_regions": {
@@ -331,7 +331,7 @@ class DockerContainers(StrEnum):
             "dir_name": "genome",
         },
         "rank_score": {
-            "url": "https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/cancer/rank_model/cancer_rank_model_-v0.1-.ini",
+            "url": "https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/cancer/rank_model/cancer_rank_model_-v0.2-.ini",
             "file_type": FileType.TXT,
             "gzip": False,
             "file_name": "cancer_rank_model_-v0.1-.ini",

BALSAMIC/containers/annotate/Dockerfile

@@ -1,32 +1,34 @@
-FROM continuumio/miniconda3:4.10.3-alpine
+FROM continuumio/miniconda3:25.1.1-2
 
-LABEL base.image="continuumio/miniconda3:4.10.3-alpine"
-LABEL about.home="https://github.com/Clinical-Genomics/BALSAMIC"
-LABEL about.documentation="https://balsamic.readthedocs.io/"
-LABEL about.license="MIT License (MIT)"
-LABEL about.maintainer="Khurram Maqbool khurram dot maqbool at scilifelab dot se"
-LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
+LABEL base.image="continuumio/miniconda3" \
+    maintainer="Clinical Genomics" \
+    about.contact="[email protected]" \
+    about.license="MIT License (MIT)" \
+    about.home="https://github.com/Clinical-Genomics/BALSAMIC" \
+    about.documentation="https://balsamic.readthedocs.io/" \
+    about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
 
-ENV PATH="/opt/conda/bin/:${PATH}"
+ARG CONTAINER_NAME
 
-RUN apk add --no-cache bash gcc git zlib-dev musl-dev
+# Copy enviroment file
+COPY BALSAMIC/containers/${CONTAINER_NAME}/${CONTAINER_NAME}.yaml /tmp/environment.yaml
 
-ARG WORK_DIR=project
-ARG CONTAINER_NAME
+# Create conda environment
+RUN conda env create -n ${CONTAINER_NAME} -f /tmp/environment.yaml && \
+    conda clean -afy && \
+    rm -f /tmp/environment.yaml
 
-# Copy all project files
-COPY . /${WORK_DIR}
+ENV PATH="/opt/conda/envs/${CONTAINER_NAME}/bin/:${PATH}"
 
-RUN apk add --no-cache make
+# Run as a non-root
+RUN useradd -m dockeruser
+USER dockeruser
 
-RUN cd /opt \
-    && git clone https://github.com/lgmgeo/AnnotSV.git \
-    && cd /opt/AnnotSV/  \
-    && git checkout v3.1.3 \
-    && make PREFIX=. install \
-    && export ANNOTSV=/opt/AnnotSV
+# Set the work directory
+WORKDIR /home/dockeruser/
 
-RUN cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
+# Set the default shell
+SHELL ["/bin/bash", "-c"]
 
-# Clean work environment
-RUN rm -rf /${WORK_DIR} && conda clean --all --yes
+# Define the default command
+CMD ["/bin/bash"]