image slimming and gen3 data pull functionality (#8)

ai-readi/Dockerfile

@@ -1,5 +1,5 @@
 # use base image
-FROM quay.io/ohsu-comp-bio/bridge2ai-jupyter:restricted-gpu-root
+FROM quay.io/ohsu-comp-bio/bridge2ai-jupyter:cpu-root
 
 # return to non-root user
 USER $NB_UID
@@ -30,7 +30,18 @@ RUN git clone https://github.com/rmaphoh/AutoMorph.git && \
     pip install -r requirement.txt && \
     pip install efficientnet_pytorch
 
+# add g3t
+SHELL ["conda", "run", "-n", "base", "/bin/bash", "-c"]
+RUN pip install --upgrade pip 
+RUN pip install gen3-tracker \
+    && pip install -U gen3-tracker
+
 # allow use of conda envs
 RUN conda init bash && exec bash
 
-# USER root
+# add gen3-client
+RUN wget https://github.com/ACED-IDP/cdis-data-client/releases/latest/download/gen3-client-linux-amd64.zip \
+    && unzip gen3-client-linux-amd64.zip \
+    && mkdir ~/.gen3 \
+    && echo 'export PATH=$PATH:~/.gen3' >> ~/.bashrc \
+    && source ~/.bashrc

cm4ai/Dockerfile

@@ -1,5 +1,5 @@
 # use base image
-FROM quay.io/ohsu-comp-bio/bridge2ai-jupyter:restricted-gpu-root
+FROM quay.io/ohsu-comp-bio/bridge2ai-jupyter:cpu-root
 
 # return to non-root user
 USER $NB_UID
@@ -17,4 +17,18 @@ RUN cd b2ai-f2f/cellmaps_pipeline \
     && make dist \
     && pip install dist/cellmaps_pipeline*whl
 
-RUN conda init bash && exec bash
+# add g3t
+SHELL ["conda", "run", "-n", "base", "/bin/bash", "-c"]
+RUN pip install --upgrade pip 
+RUN pip install gen3-tracker \
+    && pip install -U gen3-tracker
+
+# allow use of conda envs
+RUN conda init bash && exec bash
+
+# add gen3-client
+RUN wget https://github.com/ACED-IDP/cdis-data-client/releases/latest/download/gen3-client-linux-amd64.zip \
+    && unzip gen3-client-linux-amd64.zip \
+    && mkdir ~/.gen3 \
+    && echo 'export PATH=$PATH:~/.gen3' >> ~/.bashrc \
+    && source ~/.bashrc

voice/Dockerfile

@@ -1,12 +1,36 @@
 # use base image
 FROM quay.io/ohsu-comp-bio/bridge2ai-jupyter:cpu-root
 
+# return to non-root user
+USER $NB_UID
+WORKDIR /home/$NB_USER
+
+# create environment
+# setup environment
+RUN conda create -n voice
+SHELL ["conda", "run", "-n", "voice", "/bin/bash", "-c"]
+RUN conda install python=3.11
 RUN pip install --no-cache-dir b2aiprep ipympl huggingface_hub[cli]
+RUN pip install ipykernel
+RUN python -m ipykernel install --user --name voice --display-name "Python (voice)"
 
 # download models
 RUN MODEL_DIR=$HOME/models && \
    huggingface-cli download --local-dir $MODEL_DIR/speechbrain/spkrec-ecapa-voxceleb speechbrain/spkrec-ecapa-voxceleb --cache-dir ${MODEL_DIR}/cache && \
    huggingface-cli download --local-dir $MODEL_DIR/openai/whisper-base openai/whisper-base --cache-dir ${MODEL_DIR}/cache
 
+# add g3t
+SHELL ["conda", "run", "-n", "base", "/bin/bash", "-c"]
+RUN pip install --upgrade pip 
+RUN pip install gen3-tracker \
+    && pip install -U gen3-tracker
+
 # allow use of conda envs
 RUN conda init bash && exec bash
+
+# add gen3-client
+RUN wget https://github.com/ACED-IDP/cdis-data-client/releases/latest/download/gen3-client-linux-amd64.zip \
+    && unzip gen3-client-linux-amd64.zip \
+    && mkdir ~/.gen3 \
+    && echo 'export PATH=$PATH:~/.gen3' >> ~/.bashrc \
+    && source ~/.bashrc