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FAQs

  Question SVG Vector Frequently asked questions

We recommend that you follow the pre-course installation instructions, which should avoid most bugs. As we are time limited, we will not be able to assist you in debugging your installations during the hands-on sessions.

 

Question SVG VectorGeneral questions

Where do I find the Zoom links? ----- If you were accepted to the course, you will be able to access the page with all the relevant links.
Where do I ask questions? ----- Please use the HackMD.

 

Docker containers 

Got permission denied while trying to connect to the Docker: ...connect: permission denied. See 'docker run --help'. ----- Make sure you are launching docker commands with sudo . For instance, sudo docker run...
I'm getting errors initializing the rstudio container. What is my username and password? -----  If you have used docker run... (the recommended solution), it should be "omics" or if doesn't work try "rstudio", and your password is set by yourself in the command. If you have built the container with docker-compose your user is "omics" and your password is omics.
I cannot see my folder within rstudio / jupyter. -----  Rstudio: make sure you set  -v /path/to/your/workshop_omics_integration:/home/omics/workshop_omics_integration/ . If this still doesn't work, replace the target path -v /path/to/your/workshop_omics_integration:/home/rstudio/workshop_omics_integration/ .
-----  Jupyter: make sure you set  -v /path/to/your/workshop_omics_integration/:/home/jovyan/workshop_omics_integration/.
What is my username and password in the jupyter container? -----  Your username is "jovyan". If you have used docker run... (the recommended solution), your password is set by yourself with the command. If you have built the container with docker-compose your user is "omics" and your password is omics.
WARNING: The requested image's platform ... does not match the detected host platform ... and no specific platform was requested 1e53..9509 -----  You need to provide the correct platform in  docker run... --platform <yourplatform> . See here Links to an external site. for an example.
Can I use normal bash commands in the containers? -----  Yes, use sudo docker run -it ... bash with any container.
How do I get the container to see a folder in my own computer? ----- When you  docker run you can map folders with  -v host_folder:folder_within_container .  For instance,   docker run -v $(PWD):/home/omics/workshop/ to map your working directory to the folder /home/omics/workshop/   inside the container.
How do I list containers and their ids? ----- Use docker ps --all.
How do I stop a running container? ----- Use docker stop [container_id].
How do I remove images, containers and volumes? ----- For images docker image rm [container_id], for containers docker container [container_id], for volumes docker volume [container_id].
How do I remove unused images, containers and volumes? ----- For images docker image prune, for containers docker container prune, for volumes docker volume prune.