OpenCGA has published a docker image for quick testing and playing without going through hassle to learn, wait and install each and every OpenCGA components. The docker image is available at the public docker registry under the repository opencb/opencga-demo.
The OpenCGA demo docker image contains the following components:
- OpenCGA binaries
- MongoDB 4.0
- Solr 6.6 (default)
- init.sh, a bash script to install OpenCGA catalog and populate data (optional)
To download OpenCGA demo image, use the command docker pull with the OpenCB repository and optionally, an OpenCGA version. For example, next command downloads the version 1.4.1 of the OpenCGA demo image:
| Code Block |
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| language | bash |
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| theme | RDark |
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| title | Downoload the OpenCGA demo image |
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$ docker pull opencb/opencga-demo:1.4.1 |
To start the OpenCGA demo container, use the command docker run. For example:
| Code Block |
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| language | bash |
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| theme | RDark |
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| title | Start the OpenCGA container (without loading demo data) |
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$ docker run --name demo -d opencb/opencga-demo:1.4.1 |
The first time you run the OpenCGA demo container, it installs the OpenCGA catalog in mongoDB, starts the REST server listening on port 9090 and finally, it starts the OpenCGA daemon. In this case, any data is loaded. If you want to load some demo data, set the option skipLoad to false that instructs OpenCGA demo container first, to download data from Corpasome project and second, to run an ETL pipeline that loads, annotates, computes statistics and indexes data into the Solr search engine. This process roughly takes 35-40 minutes depending on the internet speed and the machine specifications. Next command starts the OpenCGA container loading demo data:
| Code Block |
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| language | bash |
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| theme | RDark |
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| title | Start the OpenCGA container loading demo data |
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$ docker run --name demo -e skipLoad=false -d opencb/opencga-demo:1.4.1 |
You can connect to the OpenCGA demo container using the following command:
| Code Block |
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| theme | RDark |
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| title | Connect to the OpenCGA demo container |
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$ docker exec -it demo bash |
To fetch the logs of the OpenCGA demo container, user the following command:
| Code Block |
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| theme | RDark |
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| title | Fetch the logs of the OpenCGA demo container |
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$ docker logs demo -f |
In order to access to the Solr dashboard, use the following URL on your internet browser:
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http://OpenCGA-Demo-Container-IP:8983/solr |
OpenCGA will listen on the following address :
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http://OpenCGA-Demo-Container-IP:9090/opencga/webservices/rest/v1/users/create |
