update

jhuapl-bio · Aug 28, 2023 · 9935091 · 9935091
1 parent 7d73657
commit 9935091
Showing 1 changed file with 47 additions and 47 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -5,52 +5,52 @@ FROM nvidia/cuda:12.2.0-base-ubuntu20.04
 SHELL ["/bin/bash", "--login", "-c"]
 ARG DEBIAN_FRONTEND=noninteractive
 
-# install apt dependencies and update conda
-RUN apt-get  --allow-releaseinfo-change  update
-RUN apt-get install git -y \
-    && apt-get install -y nginx apt-transport-https ca-certificates wget unzip bzip2 libfontconfig1 && \
-    update-ca-certificates \
-    && apt-get install -y g++ gcc gawk bzip2 \
-    && apt-get -qq -y autoremove \
-    && apt-get autoclean  && \
-    apt-get install -y curl && \
-    apt-get -y install software-properties-common && add-apt-repository -y ppa:deadsnakes/ppa && apt update -y && \
-    apt-get install -y python3.8 && \
-    apt-get install -y python3-pip && \ 
-    curl -fsSL https://deb.nodesource.com/setup_17.x | bash - && \
-    apt-get install -y nodejs && \
-    ln -sf /usr/bin/python3 /usr/bin/python
-
-WORKDIR /opt
-
-# Get Guppy barcoder for demux purposes, remove the jsn files to save space. This will make basecalling unusable
-RUN wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy_6.4.6_linux64.tar.gz -O ./guppy_6_gpu.tar.gz && \
-    tar -xvzf /opt/guppy_6_gpu.tar.gz && mv /opt/ont-guppy /opt/ont-guppy-gpu  && rm /opt/guppy_6_gpu.tar.gz && \
-    wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.4.6_linux64.tar.gz -O ./guppy_6_cpu.tar.gz && \
-    tar -xvzf /opt/guppy_6_cpu.tar.gz && mv /opt/ont-guppy-cpu /opt/ont-guppy && \
-    ln -sf /opt/ont-guppy/bin/guppy_barcoder /usr/local/bin/guppy_barcoder && \
-    rm /opt/guppy_6_cpu.tar.gz && rm /opt/ont-guppy/data/*.jsn && rm /opt/ont-guppy-gpu/data/*.jsn
-
-# RUN wget https://github.com/DerrickWood/kraken2/archive/refs/tags/v2.1.3.tar.gz -O kraken2.tar.gz && \
-#     tar -xvzf kraken2.tar.gz && rm kraken2.tar.gz && \
-RUN git clone https://github.com/DerrickWood/kraken2.git --branch v2.1.3 && cd kraken2 && \
-    ./install_kraken2.sh /usr/bin/ && \
-    git clone https://github.com/jenniferlu717/KrakenTools.git && \
-    cd KrakenTools && chmod +x *.py && \
-    find . -name "*.py" -exec cp {} /usr/local/bin/ \;
-
-COPY ./package.json /opt/package.json
-RUN npm install 
-
-COPY ./babel.config.js /opt/babel.config.js
-COPY ./.eslintignore /opt/.eslintignore
-COPY ./jsconfig.json /opt/jsconfig.js
-COPY ./vue.config.docker.js /opt/vue.config.js
-COPY ./src /opt/src
-RUN npm run build
-COPY ./server /opt/server
-COPY nginx.conf /etc/nginx/nginx.conf
-RUN useradd nginx && ln -s /opt/dist /usr/share/nginx/html/mytax && chmod -R 777 /usr/share/nginx/html/mytax
-EXPOSE 80
+# # install apt dependencies and update conda
+# RUN apt-get  --allow-releaseinfo-change  update
+# RUN apt-get install git -y \
+#     && apt-get install -y nginx apt-transport-https ca-certificates wget unzip bzip2 libfontconfig1 && \
+#     update-ca-certificates \
+#     && apt-get install -y g++ gcc gawk bzip2 \
+#     && apt-get -qq -y autoremove \
+#     && apt-get autoclean  && \
+#     apt-get install -y curl && \
+#     apt-get -y install software-properties-common && add-apt-repository -y ppa:deadsnakes/ppa && apt update -y && \
+#     apt-get install -y python3.8 && \
+#     apt-get install -y python3-pip && \ 
+#     curl -fsSL https://deb.nodesource.com/setup_17.x | bash - && \
+#     apt-get install -y nodejs && \
+#     ln -sf /usr/bin/python3 /usr/bin/python
+
+# WORKDIR /opt
+
+# # Get Guppy barcoder for demux purposes, remove the jsn files to save space. This will make basecalling unusable
+# RUN wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy_6.4.6_linux64.tar.gz -O ./guppy_6_gpu.tar.gz && \
+#     tar -xvzf /opt/guppy_6_gpu.tar.gz && mv /opt/ont-guppy /opt/ont-guppy-gpu  && rm /opt/guppy_6_gpu.tar.gz && \
+#     wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.4.6_linux64.tar.gz -O ./guppy_6_cpu.tar.gz && \
+#     tar -xvzf /opt/guppy_6_cpu.tar.gz && mv /opt/ont-guppy-cpu /opt/ont-guppy && \
+#     ln -sf /opt/ont-guppy/bin/guppy_barcoder /usr/local/bin/guppy_barcoder && \
+#     rm /opt/guppy_6_cpu.tar.gz && rm /opt/ont-guppy/data/*.jsn && rm /opt/ont-guppy-gpu/data/*.jsn
+
+# # RUN wget https://github.com/DerrickWood/kraken2/archive/refs/tags/v2.1.3.tar.gz -O kraken2.tar.gz && \
+# #     tar -xvzf kraken2.tar.gz && rm kraken2.tar.gz && \
+# RUN git clone https://github.com/DerrickWood/kraken2.git --branch v2.1.3 && cd kraken2 && \
+#     ./install_kraken2.sh /usr/bin/ && \
+#     git clone https://github.com/jenniferlu717/KrakenTools.git && \
+#     cd KrakenTools && chmod +x *.py && \
+#     find . -name "*.py" -exec cp {} /usr/local/bin/ \;
+
+# COPY ./package.json /opt/package.json
+# RUN npm install 
+
+# COPY ./babel.config.js /opt/babel.config.js
+# COPY ./.eslintignore /opt/.eslintignore
+# COPY ./jsconfig.json /opt/jsconfig.js
+# COPY ./vue.config.docker.js /opt/vue.config.js
+# COPY ./src /opt/src
+# RUN npm run build
+# COPY ./server /opt/server
+# COPY nginx.conf /etc/nginx/nginx.conf
+# RUN useradd nginx && ln -s /opt/dist /usr/share/nginx/html/mytax && chmod -R 777 /usr/share/nginx/html/mytax
+# EXPOSE 80
 
 # To Run docker build . -t jhuaplbio/basestack_mytax2 ; docker container run -it --rm -p 8098:80 jhuaplbio/basestack_mytax2  bash -c "nginx; bash "