attempt to shrink q2-qiime

Author: sjanssen2

Images/qp-qiime2/qp-qiime2.dockerfile

@@ -7,16 +7,20 @@ ARG MINIFORGE_VERSION=24.1.2-0
 ENV CONDA_DIR=/opt/conda
 ENV PATH=${CONDA_DIR}/bin:${PATH}
 
-RUN apt-get -y  update
-RUN apt-get -y --fix-missing install \
-	git \
-	wget \
-	libpq-dev \
-	python3-dev \
-	gcc \
-	build-essential \
-	zip \
-	tzdata
+RUN apt-get -y  update \
+	&& apt-get install -y --no-install-recommends \
+		git \
+		wget \
+		libpq-dev \
+		python3-dev \
+		gcc \
+		build-essential \
+		zip \
+		unzip \
+		tzdata \
+		ca-certificates \
+	&& apt-get clean \
+	&& rm -rf /var/lib/apt/lists/*
 
 # install miniforge3 for "conda"
 # see https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
@@ -28,49 +32,49 @@ RUN wget https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_
 	rm -f /tmp/miniforge3.sh
 
 # install tornado based trigger layer in base environment
-RUN pip install -U pip
-RUN pip install tornado
+RUN pip install -U pip \
+	&& pip install tornado
 COPY trigger.py /trigger.py
 
-# Download qiime2 yaml
-RUN wget --quiet https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml
-
-# Create conda env
-RUN conda env create --name qiime2 -y --file qiime2-2023.5-py38-linux-conda.yml \
-  && conda clean --all -y \
-  && rm -rf /opt/conda/pkgs
+# Download qiime2 yaml and  Create conda env
+RUN wget --quiet https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml \
+	&& conda env create --name qiime2 -y --file qiime2-2023.5-py38-linux-conda.yml \
+  	&& conda clean --all -y \
+  	&& rm -rf /opt/conda/pkgs
 # Make RUN commands use the new environment:
 # append --format docker to the build command, see https://github.com/containers/podman/issues/8477
 SHELL ["conda", "run", "-p", "/opt/conda/envs/qiime2", "/bin/bash", "-c"]
 
 RUN pip install -U pip
 #RUN pip install https://github.com/qiita-spots/qiita_client/archive/master.zip
-RUN git clone -b uncouple_clientpush    https://github.com/jlab/qiita_client.git
+RUN git clone --depth 1 -b enable_pluginprotocol_change https://github.com/jlab/qiita_client.git
 RUN cd qiita_client && pip install --no-cache-dir .
-RUN pip install https://github.com/qiita-spots/qiita-files/archive/master.zip
-RUN pip install https://github.com/biocore/q2-mislabeled/archive/refs/heads/main.zip
-RUN pip install q2-umap q2-greengenes2
-#RUN git clone https://github.com/qiita-spots/qp-qiime2.git
-RUN git clone -b uncouple_clientpush https://github.com/jlab/qp-qiime2.git
+
+RUN pip install https://github.com/qiita-spots/qiita-files/archive/master.zip \
+	&& pip install https://github.com/biocore/q2-mislabeled/archive/refs/heads/main.zip \
+	&& pip install q2-umap q2-greengenes2
+
+	#RUN git clone https://github.com/qiita-spots/qp-qiime2.git
+RUN git clone --depth 1 -b uncouple_clientpush  https://github.com/jlab/qp-qiime2.git
 WORKDIR /qp-qiime2
 
 RUN sed -i "s|self.basedir, '..', '..', '|'/|g" /qp-qiime2/qp_qiime2/tests/test_qiime2.py
 
-RUN pip install -e .
-RUN pip install --upgrade certifi
-RUN pip install pip-system-certs
+RUN pip install -e . \
+	&& pip install --upgrade certifi \
+	&& pip install pip-system-certs
 
 # configuring the databases available for QIIME 2
-RUN mkdir /databases
-RUN wget --quiet -O "/databases/gg-13-8-99-515-806-nb-classifier.qza" "https://data.qiime2.org/2021.4/common/gg-13-8-99-515-806-nb-classifier.qza"
-RUN export QP_QIIME2_DBS=/databases
+RUN mkdir /databases \
+	&& wget --no-check-certificate --quiet -O "/databases/gg-13-8-99-515-806-nb-classifier.qza" "https://data.qiime2.org/2021.4/common/gg-13-8-99-515-806-nb-classifier.qza" \
+	&& export QP_QIIME2_DBS=/databases
 
 # configuring the filtering QZAs available for QIIME 2
-RUN mkdir /filtering
-RUN wget -O /filtering/bloom-analyses.zip https://github.com/knightlab-analyses/bloom-analyses/archive/refs/heads/master.zip \
-  && unzip -j /filtering/bloom-analyses.zip bloom-analyses-master/data/qiime2-artifacts-for-qiita/*.qza -d /filtering/ \
-  && rm -f /filtering/bloom-analyses.zip
-RUN export QP_QIIME2_FILTER_QZA=/filtering/
+RUN mkdir /filtering \
+	&& wget --no-check-certificate -O /filtering/bloom-analyses.zip https://github.com/knightlab-analyses/bloom-analyses/archive/refs/heads/master.zip \
+  	&& unzip -j /filtering/bloom-analyses.zip bloom-analyses-master/data/qiime2-artifacts-for-qiita/*.qza -d /filtering/ \
+  	&& rm -f /filtering/bloom-analyses.zip \
+	&& export QP_QIIME2_FILTER_QZA=/filtering/
 
 # TODO: should the plugin get the server configuration?!
 RUN export QIITA_CONFIG_FP=/qiita/config_qiita_oidc.cfg
@@ -83,8 +87,8 @@ ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
 
 # configure timezone
-RUN ln -fs /usr/share/zoneinfo/Etc/UTC /etc/localtime
-RUN dpkg-reconfigure -f noninteractive tzdata
+RUN ln -fs /usr/share/zoneinfo/Etc/UTC /etc/localtime \
+	&& dpkg-reconfigure -f noninteractive tzdata
 
 
 WORKDIR /
@@ -105,8 +109,8 @@ RUN chmod u+x /qp-qiime2/scripts/configure_qiime2 /qp-qiime2/scripts/start_qiime
 ENV QP_QIIME2_DBS=/databases
 ENV QP_QIIME2_FILTER_QZA=/filtering/
 COPY qiita_server_certificates/*_server.* /qiita_server_certificates/
-RUN /qp-qiime2/scripts/configure_qiime2 --env-script 'true' --server-cert `find /qiita_server_certificates/ -name "*_server.crt" -type f` https
-RUN sed -i -E "s/^START_SCRIPT = .+/START_SCRIPT = python \/start_plugin.py qp-qiime2/" /unshared_plugins/*.conf
+RUN /qp-qiime2/scripts/configure_qiime2 --env-script 'true' --server-cert `find /qiita_server_certificates/ -name "*_server.crt" -type f` https \
+	&& sed -i -E "s/^START_SCRIPT = .+/START_SCRIPT = python \/start_plugin.py qp-qiime2/" /unshared_plugins/*.conf
 
 # for testing
 COPY test_plugin.sh /test_plugin.sh