Merge branch 'master' of github.com:fuxialexander/getdemo

.github/workflows/docker-build-and-push.yml

@@ -32,4 +32,5 @@ jobs:
       with:
         context: .
         push: true
+        file: ./Dockerfile-dockerhub
         tags: fuxialexander/getdemo:latest

Dockerfile

@@ -1,60 +1,16 @@
-# Use an official miniconda3 as a parent image
-FROM mambaorg/micromamba
+# This is the dockerfile for the Gradio app on huggingface
+FROM fuxialexander/getdemo:latest
 
-
-USER root
-RUN usermod -u 1000 $MAMBA_USER
+# Switch to mambauser with updated UID
 USER $MAMBA_USER
-
 # Set the working directory in the container to /app
 WORKDIR /app
-# Create a new environment using mamba with specified packages
-RUN micromamba install -n base -c conda-forge -c bioconda -y python=3.10 pip biopython s3fs
-RUN micromamba install -n base -c conda-forge -c bioconda -y nglview tqdm matplotlib pandas 
-RUN micromamba install -n base -c conda-forge -c bioconda -y openpyxl pyarrow python-box xmlschema seaborn numpy py3Dmol pyranges scipy pyyaml zarr numcodecs 
-RUN micromamba install -n base -c conda-forge -c bioconda -y pybigwig networkx plotly pysam requests seqlogo MOODS urllib3 pyliftover gprofiler-official pyfaidx
-RUN micromamba install -n base -c conda-forge -y dash-bio
 
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
-# Activate the environment and install additional packages via pip
-RUN pip3 install gradio  
-USER root
-RUN mkdir /data
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    git \
-    ssh \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/*
-
-USER $MAMBA_USER
-
-# copy modules from local to container
-COPY --chown=$MAMBA_USER:$MAMBA_USER modules /app/modules
-
-# copy modules from local to container
-COPY --chown=$MAMBA_USER:$MAMBA_USER app /app/app
-
-# copy modules from local to container
-# COPY --chown=$MAMBA_USER:$MAMBA_USER data /app/data
 
-# Clone a specific git repository and install it as an editable package
-
-RUN cd modules/proscope &&  \
-    pip3 install .
-
-RUN cd modules/atac_rna_data_processing &&  \
-    pip3 install .
-
-# clean all mamba caches and remove unnecessary files
-RUN micromamba clean --all --yes
-
-
-
-WORKDIR /app
+COPY --chown=$MAMBA_USER:$MAMBA_USER app/main.py /app/app/main.py
 
-# Make port 80 available to the world outside this container
-EXPOSE 7860
 # Set the working directory where your app resides
 
 # Command to run the Gradio app automatically
-CMD ["python", "app/main.py", "-p", "7860", "-s", "-u", "s3://2023-get-xf2217/get_demo_test_data", "-d", "/data"]
+CMD ["python", "/app/app/main.py", "-n", "0.0.0.0", "-p", "7860", "-u", "s3://2023-get-xf2217/get_demo_test_data", "-d", "/app/data"]

Dockerfile-dockerhub

@@ -0,0 +1,60 @@
+# This is the dockerfile for dockerhub fuxialexander/getdemo:latest
+FROM mambaorg/micromamba
+
+
+USER root
+RUN usermod -u 1000 $MAMBA_USER
+USER $MAMBA_USER
+
+# Set the working directory in the container to /app
+WORKDIR /app
+# Create a new environment using mamba with specified packages
+RUN micromamba install -n base -c conda-forge -c bioconda -y python=3.10 pip biopython s3fs
+RUN micromamba install -n base -c conda-forge -c bioconda -y nglview tqdm matplotlib pandas 
+RUN micromamba install -n base -c conda-forge -c bioconda -y openpyxl pyarrow python-box xmlschema seaborn numpy py3Dmol pyranges scipy pyyaml zarr numcodecs 
+RUN micromamba install -n base -c conda-forge -c bioconda -y pybigwig networkx plotly pysam requests seqlogo MOODS urllib3 pyliftover gprofiler-official pyfaidx
+RUN micromamba install -n base -c conda-forge -y dash-bio
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+# Activate the environment and install additional packages via pip
+RUN pip3 install gradio  
+USER root
+RUN mkdir /data
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git \
+    ssh \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+USER $MAMBA_USER
+
+# copy modules from local to container
+COPY --chown=$MAMBA_USER:$MAMBA_USER modules /app/modules
+
+# copy modules from local to container
+COPY --chown=$MAMBA_USER:$MAMBA_USER app /app/app
+
+# copy modules from local to container
+# COPY --chown=$MAMBA_USER:$MAMBA_USER data /app/data
+
+# Clone a specific git repository and install it as an editable package
+
+RUN cd modules/proscope &&  \
+    pip3 install .
+
+RUN cd modules/atac_rna_data_processing &&  \
+    pip3 install .
+
+# clean all mamba caches and remove unnecessary files
+RUN micromamba clean --all --yes
+
+
+
+WORKDIR /app
+
+# Make port 80 available to the world outside this container
+EXPOSE 7860
+# Set the working directory where your app resides
+
+# Command to run the Gradio app automatically
+CMD ["python", "app/main.py", "-p", "7860", "-s", "-u", "s3://2023-get-xf2217/get_demo_test_data", "-d", "/data"]

modules/proscope

@@ -1 +1 @@
-Subproject commit f347e71b75ab5b7afd58134e53cc60a1b762f562
+Subproject commit f724f8bbc6d9e132c656fc21e854e394755f89db