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hurwitzlab / funannotate

Stampede2 implementation of https://github.com/nextgenusfs/funannotate
MIT License
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how to configure funannotate in singularity image? #1

Open rbatorsky opened 5 years ago

rbatorsky commented 5 years ago

I came upon this while searching for singularity recipes for funannotate. I'm trying to install funannotate on an HPC cluster using singularity, without root or docker available. The steps in the Dockerfile that funannotate provides are giving me some trouble with funannotate, e.g. configuring repeatmasker/repeatmodler and downloading the funannotate databases. Do you have any advice about how to accomplish these steps when using singularity? I don't see those steps in the singularity def file in this repository, so I'm wondering if you managed to do them outside the container and bind them later. Thanks for any advice.

kyclark commented 5 years ago

I've never tried to build the tools inside funannotate, so I can't help you there. You can see how simple my Singularity definition is because I am able to build on the existing Docker def. I can't see how you're able to use Singularity if you don't have root. What problems are you having?