Merge pull request #5 from ohsu-comp-bio/cm4ai

CM4AI Image
ohsu-comp-bio · Apr 16, 2024 · e181597 · e181597
2 parents 1d503d3 + 4c86242
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diff --git a/cm4ai/Dockerfile b/cm4ai/Dockerfile
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+# 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
diff --git a/cm4ai/README.md b/cm4ai/README.md
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+# 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.
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		# 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.