Closed tbazilegith closed 1 year ago
May I run Pgap this way at all?
I do not think we support this way.
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?
Is that something pgap support?
I do not think so.
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.
— Reply to this email directly, view it on GitHubhttps://github.com/ncbi/pgap/issues/246#event-8889548256, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALBJ5RRNYNN2ZYDIBQNNSW3W6WXKLANCNFSM6AAAAAAVWW6C3Y. You are receiving this because you authored the thread.Message ID: @.***>
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: