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ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
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pgap.py not found with docker container ncbi/pgap #268

Closed tbazilegith closed 5 months ago

tbazilegith commented 11 months ago

Hi Azat, Describe the bug I pulled the container to run run pgap in nextflow container = 'ncbi/pgap'

To Reproduce /ERROR ~ Error executing process > 'ani'

Caused by: Failed to pull singularity image command: singularity pull --name ncbi-pgap-dev.img.pulling.1692838424330 docker://ncbi/pgap-dev > /dev/null status : 255 message: FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ncbi/pgap-dev: reading manifest latest in docker.io/ncbi/pgap-dev: manifest unknown: manifest unknown

Expected behavior Singularity cache directory has not been defined -- Remote image will be stored in the path: my_path/work/singularity

Thanks, TJ

tbazilegith commented 11 months ago

There are several containers on dockerhub. Which one is the right one? After pulling the container, how to get executable pgap.py? Thanks!

thibaudnis commented 11 months ago

Hi TJ - not sure what you are trying to do. Please start with https://github.com/ncbi/pgap/wiki/Quick-Start for getting pgap.py and getting started, and consult our FAQs as needed: https://github.com/ncbi/pgap/wiki/FAQ. Thanks!

tbazilegith commented 11 months ago

Thanks Thilbaudnis, I emplemented pgap in a nexflow, and I pulled the container from dockerhub, expecting run pgap onces the container is copied. Based on your recommendation, we don't need to pull container directly from dockerhub, but only follow the github installation? Thanks

azat-badretdin commented 11 months ago

That should be enough