Download a model behing a corporative proxy

[enekomatute]

Hello,

My name is Eneko and maybe i can get some help to solve this problem with medaka. I don't know if it's the right place to post this but I don't know where else to do it.

I'm new to this, starting with Epi2me on Ubuntu and trying to test the epi2me-labs/wf-bacterial-genomes v0.2.11 workflow. I keep having the same error.

[c4/92af38] Submitted process > calling_pipeline:medakaNetwork (1) Error executing process > 'calling_pipeline:medakaNetwork (1)' Caused by: Process calling_pipeline:medakaNetwork (1) terminated with an error exit status (1) Command executed: medaka --version echo r1041_e82_400bps_hac_g615

  echo r1041_e82_400bps_hac_g615

.............. File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/medaka.py", line 38, in call raise RuntimeError(msg.format(self.dest, str(e))) RuntimeError: Error validating model from '--model' argument: The model file for r1041_e82_400bps_hac_g615 is not already installed and could not be downloaded. Check you are connected to the internet and try again.. Work dir:

I have configured then proxy like enviroment variables for docker; Lowercase and UPppercase, but i still get the same error. I think the problem is that I can`t configure medaka for download the model request thorugh the coportative proxy. Any ideas to solve it?

Thank you.

[cjw85]

Hi @enekomatute,

Thank you for reporting this. It was intended that the docker images used in wf-bacterial-genomes should contain all the medaka models, negating the need for them to be downloaded on the fly. It seems this wasnt implemented. We will rectify that.

[hkaspersen]

Hello! I am having similar difficulties, as I am running it on an HPC cluster with no internet connection. Making the models available in the image sounds like an excellent fix, when can we expect this to be available?

[cjw85]

I believe the images have now been updated with a more complete set of models.