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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Exomiser Cli Version 14.00 Distroless Internal Singularity Path #572

Open yr542 opened 6 days ago

yr542 commented 6 days ago

I am having difficulty looking inside the Exomiser singularity and I cannot seem to run it despite the singularity being installed:

singularity exec \
  --bind "/path/to/directory/containing/vcfs/directory" \
  --bind  "/path/to/output/directory" \
  "/path/to/exomiser-cli_14.0.0-distroless.sif" \
  java -Xms4g -Xmx8g -jar "/exomiser-cli.jar" \
  --analysis "/path/to/pilot/file.yml"

It seems to run bit and then I get the following errors:

Error: Unable to access jarfile /exomiser-cli.jar

Could get the internal path of the singularity? I cannot seem to get the command to run without it?

julesjacobsen commented 4 days ago

I haven't tried running this with Singularity - can you use Docker/Podman with this image? Alternatively, there is the Debian based version with a shell: docker pull exomiser/exomiser-cli:14.0.0