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CirclatorΒΆ

Circlator is made available as an Apptainer container.

You can direcly run 'circlator' from the container with:

Terminal

circlator_1.5.5.sif circlator test outdir

Alternatively you can enter an interactive shell in the container with:

Terminal

circlator-1.5.5.sif /bin/bash

and run circlator from there.

This assumes all input and output files are located in your home directory, which gets automatically made available in the container by Apptainer. Other paths will have to be explicitely mapped, in which case we need to use the apptainer run command excplictely pointing to the location of the container image. e.g. to map the /scratch/foo/data directory on /data in the container:

Terminal

apptainer run --bind /tmp/test $APPTAINER_IMAGES/circlator_1.5.5.sif circlator test /tmp/test/outdir