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bordin89 / ICB_docker

Docker image and scripts for ICB
GNU General Public License v3.0
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No file in /data/ #1

Open sarah872 opened 5 years ago

sarah872 commented 5 years ago

I am running docker toolbox because on Windows 10 Home, and I am experiencing an issue when running the command

docker run -it -v /d/data/uniprot.fasta:/data/ bordin89/icb

and the docker container is starting, but there is no uniprot.fasta file in /data. Do you have any ideas how to troubleshoot?

bordin89 commented 5 years ago

Hi! I just checked on my setup and it works using an absolute path, while it fails using a local path. I'll update the documentation.

In my case I run "sudo docker run -it -v /home/user/dockerfiles/test/:/data/ bordin89/icb" And I can find all the files in the folder "test". Does docker have the permissions to access the data? Are you using an absolute path?

Let me know how it goes!

sarah872 commented 5 years ago

Thanks for the very quick answer! I think Windows is here a bit more complicated. I have to drives, C: and D:, and I have my data on D: in a folder data. I am specifying the absolute (WIndows-written) path as stated above.

When I try with files on C:, I am getting a Permission denied error. Unfortunately sudo does not work on docker toolbox. But I think it should work with my data on D:, too!

bordin89 commented 5 years ago

No problem! Have you tried running the Docker container as administrator? You can do this using the run-as-command with an administrator trust-level, or by right-clicking the program in the UI and choosing "run as administrator. I'll try to dig in some more, but unfortunately I'm out of the lab until the 4th of January. Let me know how it goes with "run as administrator".

sarah872 commented 5 years ago

there is no sudo on docker toolbox. I tried running the UI as administrator and there is no error when running the docker run, but still there are no files in /data on the docker-container. I will also be leaving for vacations, so, no worries! thanks!

bordin89 commented 5 years ago

I found this, hopefully it helps! https://rominirani.com/docker-on-windows-mounting-host-directories-d96f3f056a2c