image: first prototype

tesp-image/Dockerfile

@@ -0,0 +1,37 @@
+FROM ubuntu:22.04
+
+RUN apt update && apt install -y --no-install-recommends \
+	gzip \
+	curl \
+	wget \
+	python3 \
+	python3-pip \
+	python-is-python3
+
+RUN pip3 install pulsar-client
+
+RUN pip3 install --upgrade pip &&     pip3 install galaxy-app &&     pip3 install galaxy-tool-util &&     pip3 install galaxy-util &&     pip3 install requests &&     pip3 install requests-toolbelt &&     pip3 install pulsar-galaxy-lib
+
+# Required by mamba
+RUN apt install -y --no-install-recommends \
+	libarchive13
+
+RUN cd /tmp && \
+	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+	bash Miniconda3-latest-Linux-x86_64.sh -b -p "/opt/miniconda3"
+
+RUN /opt/miniconda3/bin/conda install -c conda-forge mamba
+ENV PATH="/opt/miniconda3/bin/:${PATH}"
+
+RUN mamba create -n "__fastqc@0.11.9" -c bioconda fastqc=0.11.9 -y
+#RUN mamba install -c bioconda fastqc -y
+
+RUN mkdir -p /home/ubuntu/galaxy/database/dependencies/
+RUN ln -s /opt/miniconda3 /home/ubuntu/galaxy/database/dependencies/_conda
+
+COPY docker-entrypoint.sh /
+RUN chmod +x /docker-entrypoint.sh
+
+ENTRYPOINT ["/docker-entrypoint.sh"]
+#ENTRYPOINT ["sleep", "infinity"]
+

tesp-image/build.sh

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+docker build -t hub.cerit.io/josef_handl/gtdi .
+docker push hub.cerit.io/josef_handl/gtdi
+

tesp-image/docker-entrypoint.sh

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+#!/bin/bash
+
+set -x
+
+echo "command: \"$@\""
+
+
+check_file() {
+	file_to_check="/opt/f"
+	interval=5  # Time interval in seconds
+
+	while true; do
+		if [ -f "$file_to_check" ]; then
+			echo "File exists. Exiting..."
+			exit 0
+		fi
+		sleep "$interval"
+	done
+}
+
+
+#sleep 10
+#sh -c "$@"
+#sleep infinity # <---
+
+
+
+
+check_file
+
+
+
+#exec $@ # <---
+
+#while [ ! -f "/ok" ]; do
+#	sleep 1
+#done
+
+#sleep infinity
+
+