run it without docker

[iranmdl]

Hi!

I work on a remote server where neither Docker nor an internet connection is available. I want to use methylr with singularity.

I created a singularity image on my local linux machine running:

singularity build --bind /tmp/shiny-server.dvmaGo/logs:/var/log/shiny --bind /tmp/shiny-server.dvmaGo/lib:/var/lib/shiny-server --bind shiny-server.conf:/etc/shiny-server/shiny-server.con methylr.simg docker://jd21/methylr:latest

And then I imported the image methylr.simg to the remote server.

I executed the image running:

singularity run --bind /tmp/shiny-server.dvmaGo/logs:/var/log/shiny --bind /tmp/shiny-server.dvmaGo/lib:/var/lib/shiny-server --bind shiny-server.conf:/etc/shiny-server/shiny-server.con methylr.simg

When I open localhost:IP I read:

An error has occurred
The application failed to start.
The application exited during initialization.

In the terminal I can read the following:

[INFO] shiny-server - Error getting worker: Error: The application exited during initialization.

Is there any workaround?

Irantzu

[JD2112]

Hi Irantzu, Is there a typo --bind shiny-server.conf:/etc/shiny-server/shiny-server.con? I have seen lot of difficulties while running shiny-server with Singularity container in clusters or HPCs. However, I think it should work when you add shiny-server.conf with the container. I think the error occurs because the shiny-server fails to recognise the on the machine. Please make sure if your config file has run as shiny as run as <USERNAME>. It would be great to know if this works.