add build on debian 11 / python 3.9 for future release

Dockerfile-deb11

@@ -0,0 +1,141 @@
+FROM debian:bullseye
+
+WORKDIR /root
+ENV BIOMAJ_CONFIG=/root/config.yml
+ENV prometheus_multiproc_dir=/tmp/biomaj-prometheus-multiproc
+
+RUN rm -rf /tmp/biomaj-prometheus-multiproc
+RUN mkdir -p /tmp/biomaj-prometheus-multiproc
+
+RUN apt-get update && apt-get install -y apt-transport-https curl libcurl4-openssl-dev python3-pycurl python3-setuptools python3-pip git unzip bzip2 ca-certificates jq --no-install-recommends
+
+# Install docker to allow docker execution from process-message
+RUN buildDeps='gnupg2 dirmngr software-properties-common' \
+    && set -x \
+    && apt-get install -y $buildDeps --no-install-recommends \
+    && curl -fsSL https://download.docker.com/linux/debian/gpg | apt-key add - \
+    && add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable" \
+    && apt-get update \
+    && apt-get install -y docker-ce-cli \
+    && apt-get purge -y --auto-remove $buildDeps
+
+ENV BIOMAJ_RELEASE="shahikorma-v14-deb11"
+
+RUN git clone https://github.com/genouest/biomaj-core.git
+#RUN easy_install3 pip
+RUN pip3 install setuptools --upgrade
+
+RUN git clone https://github.com/genouest/biomaj-zipkin.git
+
+RUN git clone https://github.com/genouest/biomaj-user.git
+
+RUN git clone https://github.com/genouest/biomaj-cli.git
+
+RUN git clone https://github.com/genouest/biomaj-process.git
+
+RUN git clone https://github.com/genouest/biomaj-download.git
+
+RUN git clone  https://github.com/genouest/biomaj.git && echo "Install biomaj"
+
+RUN git clone https://github.com/genouest/biomaj-daemon.git && echo "Install daemon"
+
+RUN git clone https://github.com/genouest/biomaj-watcher.git && echo "Install biomaj-watcher"
+
+RUN git clone https://github.com/genouest/biomaj-ftp.git
+
+RUN git clone https://github.com/genouest/biomaj-release.git
+
+RUN git clone https://github.com/genouest/biomaj-data.git
+
+ENV BIOMAJ_CONFIG=/etc/biomaj/config.yml
+
+RUN mkdir -p /var/log/biomaj
+
+#RUN pip3 install greenlet==0.4.17
+#RUN pip3 install gevent==1.4.0
+RUN pip3 install graypy
+#RUN pip3 install pymongo==3.12.3
+#RUN pip3 install redis==3.5.3
+RUN pip3 install wheel
+#RUN pip3 install PyYAML==5.3.1
+
+ENV SUDO_FORCE_REMOVE=yes
+RUN buildDeps='gcc python3-dev protobuf-compiler' \
+    && set -x \
+    && apt-get install -y $buildDeps --no-install-recommends \
+    && cd /root/biomaj-core && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-zipkin && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-user && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-cli && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-process/biomaj_process/message && protoc --python_out=. procmessage.proto \
+    && cd /root/biomaj-process && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-download/biomaj_download/message && protoc --python_out=. downmessage.proto \
+    && cd /root/biomaj-download && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-daemon && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-watcher && pip3 install -r requirements.txt && pip3 install . \
+    && cd /root/biomaj-ftp && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-release && python3 setup.py build && pip3 install . \
+    && cd /root/biomaj-data && python3 setup.py build && pip3 install . \
+    && apt-get install -y wget bzip2 ca-certificates curl git \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && apt-get purge -y --auto-remove $buildDeps
+
+
+
+#RUN apt-get update --fix-missing && \
+#    apt-get install -y wget bzip2 ca-certificates curl git && \
+#    apt-get clean && \
+#    rm -rf /var/lib/apt/lists/*
+#RUN pip3 uninstall -y gunicorn && pip3 install gunicorn==19.9.0
+#RUN pip3 uninstall -y greenlet && pip3 install greenlet==0.4.15
+#RUN pip3 uninstall -y gevent && pip3 install gevent==1.3.7
+
+
+
+#Conda installation and give write permissions to conda folder
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh &&  \
+    /opt/conda/bin/conda config --add channels r  && \
+    /opt/conda/bin/conda config --add channels bioconda  && \
+    /opt/conda/bin/conda upgrade -y conda  && \
+    chmod 777 -R /opt/conda/
+
+
+
+
+RUN mkdir /data /config
+
+ENV PATH=$PATH:/opt/conda/bin
+
+#RUN conda config --add channels r
+#RUN conda config --add channels bioconda
+#RUN conda upgrade -y conda
+
+VOLUME ["/data", "/config"]
+
+RUN mkdir -p /var/lib/biomaj/data
+
+COPY biomaj-config/config.yml /etc/biomaj/config.yml
+COPY biomaj-config/global.properties /etc/biomaj/global.properties
+COPY biomaj-config/production.ini /etc/biomaj/production.ini
+COPY biomaj-config/gunicorn_conf.py /etc/biomaj/gunicorn_conf.py
+COPY watcher.sh /root/watcher.sh
+
+# Local test configuration
+RUN mkdir -p /etc/biomaj/conf.d
+RUN mkdir -p /var/log/biomaj
+RUN mkdir -p /etc/biomaj/process.d
+RUN mkdir -p /var/cache/biomaj
+RUN mkdir -p /var/run/biomaj
+COPY test-local/etc/biomaj/global_local.properties /etc/biomaj/global_local.properties
+COPY test-local/etc/biomaj/conf.d/alu.properties /etc/biomaj/conf.d/alu.properties
+
+# Plugins
+RUN cd /var/lib/biomaj && git clone https://github.com/genouest/biomaj-plugins.git plugins
+
+ADD https://github.com/ufoscout/docker-compose-wait/releases/download/2.6.0/wait /wait
+RUN chmod +x /wait
+COPY startup.sh /startup.sh