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
> 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.
> 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:
conda clean -a -y;
mamba install -c conda-forge [package name] --force-reinstall. If you get an error
Problem: nothing provides requested [package nameplease search for it in anaconda cloud and change the channel accordingly (e.g. one of
-c [bioconda | r | rdonnelly ]);
> Command line developer tools not found (OSX)
If you don’t yet have Mac OSX command line developer tools, please install it using:
> 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.