Require both singularity & manual software installation

StepanSaenko / varus-braker

Small pipeline combining raw genome-data and VARUS.bam (or RNA-seq data) and run BRAKER3

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Require both singularity & manual software installation #1

Open KatharinaHoff opened 1 year ago

KatharinaHoff commented 1 year ago

suggestion: put all required software into docker containers/user existing docker containers for all pipeline steps. I can help with that.

KatharinaHoff commented 1 year ago

Here's what I think is the full list of software requirements:

BRAKER (container integrated)
RepeatModeler2/RepeatMasker: docker://dfam/tetools:latest (we may not want to use latest, maybe fix a version; I have tested this container)
BUSCO: docker://quay.io/biocontainers/busco:latest (see above, I have not tested this container)
VARUS + OMArk need to be in a novel container. I will prepare this.

KatharinaHoff commented 1 year ago

I prepared a container for testing that should have both BRAKER (incl ETP) and OMArk: https://hub.docker.com/r/katharinahoff/bioinformatics-notebook If you find that it works for these tools, you can remove the BRAKER container. Still working on other containers.