compbiocore/VariantVisualization.jl

Issue running viva on Ubuntu

frankiefattorini opened this issue · 4 comments

Hello

I'm trying to use the viva command to visualise SNP positions in Ubuntu. I've downloaded and run julia (version 1.7.3) and I've attempted to install VariantVisualisation. It seems to have worked (although my computer keeps crashing mid-way through). When I try to run viva, I get the error message /usr/bin/env: ‘julia’: No such file or directory. Is there a known solution for this?

Thank you

Hi, I was just installing this on Ubuntu myself - the installation kind of fails because it cannot create a symbolic link in a location that requires sudo:

ERROR: Error building `VariantVisualization`: 
ERROR: LoadError: IOError: symlink("/home/jena/.julia/packages/VariantVisualization/1yoNl/viva", "/usr/local/bin/viva"): permission denied (EACCES)

So you can make the link manually and it will work. I actually did not want to use sudo, so I chose a different location in my PATH:

ln -s /home/jena/.julia/packages/VariantVisualization/1yoNl/viva ~/bin/viva

Note that ~/bin is in my PATH, so the system will find the executable and run it. On Ubuntu, this folder is included in PATH by default, you may just need to create the folder in your home directory, before making the symlink.

I still have some problems with dependencies, but at least now viva is installed in my PATH and I can run it...

Thank you, I'll give that a go and see how it runs

I got around this issue by launching the julia console with sudo:

sudo julia
]add VariantVisualization

@nahanoo Interesting, although most users won't have sudo access at their HPC cluster. It's fine for local use I guess..