Clone git repo onto R Studio server?

[yaaminiv]

@kubu4 I'm trying to clone the CEABiGR repository onto the R Studio server on Mox (need to use Mox because Raven did not have enough memory). I added the following code to the singularity definition file:

%post
    # Install additinoal system packages in container
    # Most are needed for R/RStudio dependencies
    apt -y update
    apt -y install libxml2 libz-dev libbz2-dev liblzma-dev libxtst6 git
    git clone --recursive https://github.com/sr320/ceabigr.git

I was able to create a container, but when I launch the R Studio server I have no idea where to find the files I cloned! Is there another way to clone these files/enable the Git panel in R Studio server? I know I can always rsync the files but it would be nice to push to the repo directory from Mox.

[kubu4]

You need to provide your desired location to clone the repo.

You'd likely want to add the following above your git clone line:

mkdir --parents $HOME/gitrepos && cd $_

That will create a directory called gitrepos in your home directory and then change into that directory.

Thus, when the git clone command is executed, it will clone into $HOME/gitrepos.

In your version of the definition file above, you didn't change directories. So, my guess is that the git repo was cloned into the root directory of the container (i.e. cd /).