Update jlab - Githubissues

epaaso / sc-luca-explore

Exploring the luca dataset for building coabundance networks

0 stars 0 forks source link

Update jlab #2

Closed epaaso closed 6 months ago

epaaso commented 10 months ago

A newer jupyter lab would be able to attach to running kernels

Also extensions don't work well and a build is required.

The problem is that we have installed lots of things apart from the container to be able to run scArches and leiden.

epaaso commented 10 months ago

From #1, we know the way to start is a container that starts:

[x] '--gpus all' flag activated
[x] 'scArches' as its first install and python 3.11.4

epaaso commented 10 months ago

The scArches auto annotation runs with the image netopaas/sc_arches, but we still have to install al the other packages for the whole workflow to work.

epaaso commented 8 months ago

This has been done in the netopaas/comp-onco image.

Must copy the dokcerfile to this repo