Frequently asked questions

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

Questions within Docker containers

> docker: 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 ...

> What is my username in the rstudio container?

Your user is omics. If this doesn’t work for some reason, try rstudio.

> 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 for an example.

> Can I use normal bash commands in the containers?

Yes, please use sudo docker run -it ... bash with any container. Note that you need to have -it to have an interactive tty.

> How do I make the container see a folder in my own computer?

When you do docker run ..., map the folders. For instance, docker run -v $(PWD):/omics/project/workshop/ ... to map your working directory to the folder /omics/project/workshop/ inside the container.

> How do I make RStudio see the workshop contents?

From RStudio, please run setwd('/project/'), after which you can go to File and open the notebooks normally.

Other questions

> I've installed everything through conda. Should I install instead the docker containers?

Yes, this is strongly recommended as it will avoid many bugs.

> But I'd like to keep using conda. What are common ways to solve most bugs?

Here are some helpful tips that may assist in solving installation problems or package-related bugs:

  • deactivate the environment if applicable;
  • clean cache with conda clean -a -y;
  • re-install the specific environment;
  • if the problem persists, consider installing the problematic package reported in the bug from terminal with mamba install -c conda-forge [package name] --force-reinstall. If you get an error Problem: nothing provides requested [package name please search for it in anaconda cloud and change the channel accordingly (e.g. one of -c [bioconda | r | rdonnelly ]);
  • if the problem still persists, consider installing it manually within R from CRAN or bioconductor. You’ll find all packages used at the end of each notebook and html file.
> Command line developer tools not found (OSX)

If you don’t yet have Mac OSX command line developer tools, please install it using:

  xcode-select --install
> rstudio crashes upon opening

In terminal try to open R by typing: r. Examine the returned error.

> unable to load shared object '.../R/library/igraph/libs/igraph.dylib'

In terminal, run

  mamba install -c conda-forge igraph --force-reinstall
> dyld: Library not loaded: @rpath/libncurses.6.dylib

In terminal run

  mamba install conda-forge::ncurses
> mofapy package not found.

Please install it from R with

> MOFA bugs

Refer to the MOFA repository.