exomiser/exomiser-web
Docker images of the exomiser-web from https://github.com/exomiser/Exomiser
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exomiser/exomiser-web repository overview
For information on running Exomiser itself refer to the Exomiser GitHub repository. This readme gives a overview of how to run the docker image from this repository.
To run the image you will need the standard exomiser directory layout to mount as separate volumes and
supply an application.properties file or environmental variables to point to the data required e.g.
docker run \
-v "/data/exomiser-data:/exomiser-data" \
-v "/opt/exomiser/exomiser-config/:/exomiser" \
-p 8080:8080 \
exomiser/exomiser-web:latest \
--spring.config.location=/exomiser/application.properties
or using Spring configuration arguments instead of the application.properties:
docker run -v "/data/exomiser-data:/exomiser-data" \
-p 8080:8080 \
exomiser/exomiser-web:latest \
--exomiser.data-directory=/exomiser-data \
--exomiser.hg19.data-version=2109 \
--exomiser.phenotype.data-version=2109
Here the contents of /opt/exomiser/exomiser-config is simply the application.properties file.
$ tree /opt/exomiser/exomiser-config/
exomiser-config/
└──application.properties
and the application.properties contents for hg38:
exomiser.data-directory=/exomiser-data
## hg38 config
exomiser.hg38.data-version=2109
#exomiser.hg38.remm-path=${exomiser.data-directory}/remm/ReMM.v0.3.1.post1.hg38.tsv.gz
#exomiser.hg38.local-frequency-path=${exomiser.data-directory}/local/local_frequency_test_hg38.tsv.gz
## phenotype config
exomiser.phenotype.data-version=2109
Resizing the JVM
Running a WGS analysis can take a few GB of RAM, depending on the size of the sample in question. If you need to increase the max memory of the JVM, include the following environment variable:
-e JAVA_TOOL_OPTIONS="-Xmx8G"
Tag summary
Content type
Image
Digest
sha256:daf8ce574…
Size
216.9 MB
Last updated
5 months ago
docker pull exomiser/exomiser-web