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Running Mineotaur in Docker | ||
=========================== | ||
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Clone this repository, and build the Mineotaur Docker image: | ||
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docker build -t mineotaur . | ||
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Create a Mineotaur data directory, e.g. `/mineotaur-data`, containing the properties file: | ||
- `XXX.input` | ||
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If the feature data is not provided by OMERO then also create the sample and label files: | ||
- `XXX_sample.tsv` | ||
- `XXX_labels.tsv` | ||
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Run the Docker image to create the Mineotaur data. The Mineotaur data directory must be mounted under `/mineotaur`, generated data will be written to a subdirectory in this directory named after the input screen: | ||
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docker run -v /mineotaur-data:/mineotaur mineotaur -import XXX.input | ||
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If the feature data is not provided by OMERO: | ||
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docker run -v /mineotaur-data:/mineotaur mineotaur \ | ||
-import XXX.input XXX_sample.tsv XXX_labels.tsv | ||
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You should see several log messages, ending with | ||
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INFO: Database generation finished. Start Mineotaur instance with -start YYY | ||
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where `YYY` is the name of the analysed screen. | ||
Run the Mineotaur web application, substituting `YYY`: | ||
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docker run -v /mineotaur-data:/mineotaur --start YYY | ||
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Mineotaur should be listening on port 8080 of the container. |
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FROM centos:centos7 | ||
MAINTAINER ome-devel@lists.openmicroscopy.org.uk | ||
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ENV MAVEN_VERSION=3.0.5 | ||
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RUN yum install -y java-1.8.0-openjdk-devel tar | ||
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# Don't use maven from repos because it pulls in Java 7 | ||
RUN curl -L -o apache-maven-$MAVEN_VERSION-bin.tar.gz \ | ||
http://mirror.olnevhost.net/pub/apache/maven/maven-3/$MAVEN_VERSION/binaries/apache-maven-$MAVEN_VERSION-bin.tar.gz && \ | ||
tar -zxvf apache-maven-$MAVEN_VERSION-bin.tar.gz && \ | ||
mv apache-maven-$MAVEN_VERSION /opt/maven && \ | ||
rm apache-maven-$MAVEN_VERSION-bin.tar.gz | ||
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RUN useradd build | ||
COPY . /home/build/src/ | ||
RUN chown -R build:build /home/build/src | ||
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USER build | ||
WORKDIR /home/build/src | ||
RUN /opt/maven/bin/mvn install | ||
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WORKDIR /mineotaur | ||
ENTRYPOINT ["java", "-jar", "/home/build/src/target/Mineotaur-1.0.1.jar"] | ||
CMD ["-help"] | ||
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