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Copy file name to clipboardexpand all lines: README.md
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A significant amount of development is typically required to join the MME; this has a detrimental effect on network growth. To address this and facilitate growth, we developed <i>matchbox</i> to be completely portable and easily usable in any center wishing to join the MME.
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## To use <i>matchbox</i>, you will need:
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* Java 1.8
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* Maven 3.1 (available from https://maven.apache.org/)
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* An authenticated MongoDB instance (available from https://www.mongodb.org/). This application requires a password protected MongoDB instance for tests and build to succeed (you can build without tests and MongoDB and configure MongoDB later if required as described below).
2. In the deploy/docker directory there are two files that should be handled extra carefully in production given that they will contain tokens and access information for your instance and other nodes.
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```
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config.xml : this XML file is used to configure the token to give access to your matchbox instance.
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nodes,json : this JSON file contains tokens that give your matchbox instance access to other MME nodes
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```
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Using guidance from the example data inside them, populate as needed.
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Please remember to remove default values before production!
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Possibly use a secrets-file management system to keep fully populate files that can inserted in at deployment.
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3. Then, from the matchbox docker directory, do a build (should take 6-10mins max)
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```
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docker build -t matchbox-docimg .
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```
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4. Assuming,
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* You have already downloaded the necessary reference data for Exomiser (for example to /data/reference_data/)
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* And reference data directory is accessible to Docker daemon,
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* And you have a MongoDB instance running and you have added its credentials and details to the Dockerfile before the build step,
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For example, if you are using the default HTTP settings and didn't change any port numbers:
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```
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docker run -ti -p 9020:9020 -v "/data/reference_data/":/Exomiser/matchbox/data/data matchbox-docimg
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```
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OR
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For example, if you uncommented the HTTPS settings and didn't change any HTTPS port numbers:
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```
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docker run -ti -p 8443:8443 -v "/reference_data/exomiser-cli/data":/Exomiser/matchbox/data/data matchbox-docimg
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```
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6. You can test your instance with (make sure to adjust the URL "http://localhost:9020/patient/view" with the port you used),
<i>matchbox</i> requires a reference dataset to help build it's phenotype scoring model. This dataset can be downloaded separately and mounted to the Docker container or you can rely on Docker to take care of all these details!
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1.[Build via having the reference data mounted into the container](with_data_mounted_to_container/README.md)
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2.[Rely on Docker to get the reference data into the container (Easiest)](with_data_in_container/README.md)
We are still in the process of designing a best practices build and deployment process using Docker and Kubernetes, so please consider this a work in progress.
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Please be careful to not check in Docker files with private secure
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usernames, passwords, and tokens etc.
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Please also remember to change any default passwords built into system before production!
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## To use this docker build, you will need:
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1. Docker (https://www.docker.com/)
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2. Reference data for the Exomiser dependency fetched from:
2. In the deploy/docker directory there are two files that should be handled extra carefully in production given that they will contain tokens and access information for your instance and other nodes.
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```
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config.xml : this XML file is used to configure the token to give access to your matchbox instance.
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nodes,json : this JSON file contains tokens that give your matchbox instance access to other MME nodes
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```
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Using guidance from the example data inside them, populate as needed.
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Please remember to remove default values before production!
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Possibly use a secrets-file management system to keep fully populate files that can inserted in at deployment.
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3. Then, from the matchbox docker directory, do a build (should take 6-10mins max)
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```
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docker build -t matchbox-docimg .
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```
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4. Assuming,
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* You have already downloaded the necessary reference data for Exomiser (for example to /data/reference_data/)
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* And reference data directory is accessible to Docker daemon,
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* And you have a MongoDB instance running and you have added its credentials and details to the Dockerfile before the build step,
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For example, if you are using the default HTTP settings and didn't change any port numbers:
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```
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docker run -ti -p 9020:9020 -v "/data/reference_data/":/Exomiser/matchbox/data/data matchbox-docimg
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```
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OR
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For example, if you uncommented the HTTPS settings and didn't change any HTTPS port numbers:
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```
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docker run -ti -p 8443:8443 -v "/reference_data/exomiser-cli/data":/Exomiser/matchbox/data/data matchbox-docimg
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```
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6. You can test your instance with (make sure to adjust the URL "http://localhost:9020/patient/view" with the port you used),
Copy file name to clipboardexpand all lines: deploy/maven/README.md
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## Build directly via Maven:
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To build directly via Maven, the following steps are needed. <i>matchbox</i> relies on a modified version of Exomiser (https://github.com/exomiser/Exomiser), its reference data and libraries for the phenotype matching algorithm. Given that these libraries are currently not in a maven repository, we obtain this dependency via first building Exomiser and then followed by <i>matchbox</i>. By building Exomiser first, we put its jars in the local maven repository, where the <i>matchbox</i> build is able to see and use them.
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### You will need:
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* Java 1.8
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* Maven 3.1 (available from https://maven.apache.org/)
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* An authenticated (ideally) MongoDB instance (https://www.mongodb.com/)
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### Process:
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<i>matchbox</i> relies on a modified version of Exomiser (https://github.com/exomiser/Exomiser), its reference data and libraries for the phenotype matching algorithm. Given that these libraries are currently not in a maven repository, we obtain this dependency via first building Exomiser and then followed by <i>matchbox</i>. By building Exomiser first, we put its jars in the local maven repository, where the <i>matchbox</i> build is able to see and use them.
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* Clone the Exomiser package
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- Make sure you have a settings.xml file in your ~/.m2/ directory with the following entry (to activate a local repsitory for Maven to use)
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