Getting into CryoET processing using the Relion 5 tomography pipeline.. How are people getting around the napari issues when running Relion on a cluster? (also using Mac laptop to connect) - ThreadSky

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Getting into CryoET processing using the Relion 5 tomography pipeline..

How are people getting around the napari issues when running Relion on a cluster? (also using Mac laptop to connect)

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lifeonthewedge.bsky.social•4 days ago

X forwarding won't work. You need some graphics-accelerated remote visualization platform like NICE DCV (proprietary) or OpenOnDemand + VirtualGL (free), and connect through VNC:
https://osc.github.io/ood-documentation/release-1.6/app-development/interactive/setup/modify-cluster-configuration.html
https://www.virtualgl.org/

lifeonthewedge.bsky.social•4 days ago

If that's not an option, then you're better off using some local workstation for your processing, or at least the visualization steps (mounting the cluster filesystem remotely, say)

tomo.science•4 days ago

Local workstation is our (imperfect) solution...

dabiophysicist.bsky.social•3 days ago

IMO x2go is probably an easier option for most than setting up VirtualGL from scratch

lifeonthewedge.bsky.social•3 days ago

x2go is easier, yes, but does not run OpenGL-accelerated 3D graphics. Napari for instance will not work (or will be veeery slow)

dabiophysicist.bsky.social•3 days ago

I compiled Relion on my Mac and copy minimal files to run Napari steps locally, however most rejected images are higher tilt/dose and can be excluded when extracting particle tilt series or pseudosubtomograms using the GUI options

tomaspascoa.bsky.social•3 days ago

My (also imperfect) solution is to use MobaXterm. The built-in X server works to display napari (launched on the HPC) on the local machine. I find it obviously slower than running napari locally, but good enough for this sort of application - and very easy to set up

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