diff --git a/cm4ai/Dockerfile b/cm4ai/Dockerfile new file mode 100644 index 0000000..cbd73ce --- /dev/null +++ b/cm4ai/Dockerfile @@ -0,0 +1,20 @@ +# use base image +FROM quay.io/ohsu-comp-bio/bridge2ai-jupyter:restricted-gpu-root + +# return to non-root user +USER $NB_UID +WORKDIR /home/$NB_USER + +# create environments +RUN git clone --recurse-submodules https://github.com/wadeschulz/b2ai-f2f.git +RUN cd b2ai-f2f && conda env create -f hpa_densenet.yml +RUN cd b2ai-f2f && conda env create -f perturbseq.yml +RUN cd b2ai-f2f && conda env create -f pipeline.yml + +# additional cellmap pipeline setup from readme +SHELL ["conda", "run", "-n", "cm4ai-pipeline", "/bin/bash", "-c"] +RUN cd b2ai-f2f/cellmaps_pipeline \ + && make dist \ + && pip install dist/cellmaps_pipeline*whl + +RUN conda init bash && exec bash \ No newline at end of file diff --git a/cm4ai/README.md b/cm4ai/README.md new file mode 100644 index 0000000..b6c7ec5 --- /dev/null +++ b/cm4ai/README.md @@ -0,0 +1,3 @@ +# CM4AI + +Docker file for CM4AI. Builds off `restricted-gpu-root` image, reverting use back to non-root privileges. Creates individual conda environments for hpa_densenet, perturbseq, and cellmaps pipeline. \ No newline at end of file