genopred Dockerfile

docker/Makefile

@@ -1,4 +1,4 @@
-all: hello.sif gwas.sif python3.sif r.sif
+all: hello.sif gwas.sif python3.sif r.sif genopred.sif
 
 %.sif: dockerfiles/%/Dockerfile
 	scripts/build_docker.sh $* && \

docker/dockerfiles/genopred/Dockerfile

@@ -0,0 +1,34 @@
+# gwas container
+FROM 'ubuntu:20.04'
+
+ENV TZ=Europe
+ENV DEBIAN_FRONTEND noninteractive
+
+# Essential tools
+WORKDIR /tmp
+COPY /scripts/apt_get_essential.sh .
+RUN bash apt_get_essential.sh && \
+    rm apt_get_essential.sh
+
+WORKDIR /tmp
+COPY /scripts/install_mambaforge.sh .
+RUN bash install_mambaforge.sh && \
+    rm install_mambaforge.sh
+
+WORKDIR /tools/GenoPred
+RUN git clone  --depth 1 --branch v2.2.0 https://github.com/opain/GenoPred.git .
+
+RUN conda env update -f /tools/GenoPred/pipeline/envs/pipeline.yaml
+
+# set env variables
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate genopred" >> ~/.bashrc
+
+RUN /bin/bash -c ". activate genopred && cd /tools/GenoPred/pipeline && snakemake --restart-times 3 -j 1 --use-conda --conda-frontend mamba get_dependencies"
+
+# cleanup for smaller image size
+RUN mamba clean -a -y
+RUN pip cache purge 
+
+WORKDIR /tools
+