compbiocore / VariantVisualization.jl

Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
https://compbiocore.github.io/VariantVisualization.jl/stable/
Other
85 stars 13 forks source link

Issue running viva on Ubuntu #110

Open frankiefattorini opened 2 years ago

frankiefattorini commented 2 years ago

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

janxkoci commented 2 years ago

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...

frankiefattorini commented 2 years ago

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

nahanoo commented 10 months ago

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

sudo julia
]add VariantVisualization
janxkoci commented 10 months ago

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