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Jwindler / AutoHiC

A novel genome assembly pipeline based on deep learning
https://doi.org/10.1093/nar/gkae789
MIT License
48 stars 5 forks source link

Docker Container doesn't contain the code. #8

Closed dslater82 closed 7 months ago

dslater82 commented 1 year ago

In the docker image, we have to git clone the code and activate the conda environment. The point of a docker container is to have everything in there so we can just run the program. Can you git clone the code in there.

For us on a HPC cluster, user's can not edit docker containers. We have to convert it to a singularity container anyway to make it work for us.

Thanks.

Jwindler commented 1 year ago

Thanks for your suggestion. Since AutoHiC is currently updated very fast, it is not included in the Docker image. Docker only provides a runtime environment. In addition, for cluster users, we are testing the singularity image and will release it soon.

Jwindler commented 1 year ago

Now you can follow the link https://github.com/Jwindler/AutoHiC/blob/main/example/singularity_autohic.md to run AutoHiC on the cluster. If you have any questions, feedback is welcome, thank you.

dslater82 commented 1 year ago

Thank you. I'll give the singularity image a shot.