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NCBI Prokaryotic Genome Annotation Pipeline
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Running pgap from dockerHub #246

Closed tbazilegith closed 1 year ago

tbazilegith commented 1 year ago

I tried run pgap from the docker container like this apptainer exe --cleanenv docker://ncbi/pgap:2022-12-13.build6494 -n --no-internet --ignore-all-errors -o ggap_sinDock ../../pgap_filegrouping/asb_met_dir/brucey_v2/input_brucey_v2.yaml

But I ran into this error "pgap.py": executable file not found in $PATH

Questions:

azat-badretdin commented 1 year ago

May I run Pgap this way at all?

I do not think we support this way.

tbazilegith commented 1 year ago

This container is available on dockerHub docker://ncbi/pgap:2022-12-13.build6494 I wanted run it with singularity (apptainer) Basically, this command works fine ${PGAP_INPUT_DIR}/pgap.py -n --no-internet --ignore-all-errors --container-path ${PGAP_INPUT_DIR}pgap_2022-04-14.build6021.sif -o ggap_mod_out ../pgap_filegrouping/asb_met_dir/brucey_v2/input_brucey_v2.yaml --docker singularity

-But was trying to run pgap directly from dockerHub to skip a local installation Is that something pgap support?

azat-badretdin commented 1 year ago

Is that something pgap support?

I do not think so.

tbazilegith commented 1 year ago

Thanks!

From: Azat Badretdin @.> Sent: Thursday, March 30, 2023 12:21 PM To: ncbi/pgap @.> Cc: Tassy Bazile @.>; Author @.> Subject: Re: [ncbi/pgap] Running pgap from dockerHub (Issue #246)

Closed #246https://github.com/ncbi/pgap/issues/246 as completed.

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