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blobtoolkit / blobtoolkit-docker

[Archived] Docker images for BlobToolKit
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Running snakemake pipeline with docker #6

Closed tauanajc closed 1 year ago

tauanajc commented 2 years ago

Hello there,

I have installed the entire BlobTools2 a while ago, but I keep running into issues while trying to run the snakemake pipeline, so I decided to try out docker. The staff at my institution's cluster helped me set it up with singularity, and I can run basic commands like this:

singularity exec --cleanenv blobtoolkit_2.6.5.sif blobtools -h

I would like to run the entire pipeline (I have an assembly, Illumina and ONT reads as input files). I have a config file that I created when I was trying with the full installation of blobtools and the snakemake command. But now I don't understand how to use the snakemake command with the docker version. For reference, I was using this tutorial before: https://github.com/blobtoolkit/tutorials/blob/main/2021-04-28_blobtoolkit_commandline_mollusc.md#run-blobtools-to-create-a-blobdir

Can you give an example of how to set up the snakemake pipeline with all the steps using docker please?

Thanks!

github-actions[bot] commented 1 year ago

This issue has being marked as dormant because blobtoolkit-docker is being archived. The code is now part of the main BlobToolKit repository.

If you feel the issue has not been resolved, please follow the updated BlobToolKit installation instructions to first confirm that you are using the latest version, and then open a new issue at the main BlobToolKit repository if necessary.

This issue will be automatically closed in 7 days.

github-actions[bot] commented 1 year ago

This issue was closed because it has been inactive for 7 days since being marked as dormant.