Pandas not installed in docker image

[alistairhockey]

Hi there,

I have noticed when trying to run perSVade inside the docker image that the prompt:

I believe there isn't an issue outside of the docker, so maybe pandas has been installed in the incorrect place? I am using the most up-to-date version of perSVade with the help of @robsyme

Kind regards, Alistair

[MikiSchikora]

Hi,

It seems that the conda environment perSVade_env (which contains pandas) is not activated in the interactive docker running. We developed the image to be run with docker run -i mikischikora/persvade:<tag> scripts/perSVade, so we did not consider such an interactive running.

You can type conda activate perSVade_env before /perSVade/scripts/perSVade, and this should use de correct conda environment. Does this solve the issue?

Kind regards,

Miquel Àngel Schikora Tamarit

[alistairhockey]

Hi Miquel,

It works perfectly, thank you. Glad it was a simple issue to resolve.

Kind regards, Alistair

On Thu, 13 Oct 2022 at 14:33, MikiSchikora @.***> wrote:

Hi,

It seems that the conda environment perSVade_env (which contains pandas) is not activated in the interactive docker running. We developed the image to be run with docker run -i mikischikora/persvade: scripts/perSVade, so we did not consider such an interactive running.

You can type conda activate perSVade_env before /perSVade/scripts/perSVade, and this should use de correct conda environment. Does this solve the issue?

Kind regards,

Miquel Àngel Schikora Tamarit

— Reply to this email directly, view it on GitHub https://github.com/Gabaldonlab/perSVade/issues/6#issuecomment-1277097736, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3SQS6DM7K2KOJ4DHKHCHPTWC6UMZANCNFSM6AAAAAARDYOEL4 . You are receiving this because you authored the thread.Message ID: @.***>

[MikiSchikora]

Hi,

Great. I am happy to see that it works!

Kind regards,

Miquel Àngel Schikora Tamarit