Wouter Saelens

Hi Florian Thanks for trying out the package! Could you perhaps tell me whether the .singularity folder exists, and which files it contains? Wouter

No problem! Could you maybe first try `dynwrap::test_singularity_installation(detailed = TRUE)` to make sure singularity is working fine? Thanks!

Hi @FloWuenne Something is going wrong while pulling the container (which is also the reason you don't see any output). Could you try to do `singularity exec 'docker://dynverse/ti_slingshot:v0.9.9' echo hi`...

Hi all I'm indeed afraid this indeed has something to do with how the HPC is configures and/or some bugs inside of singularity. For example, within our HPC: - Login/submit...

Yes, that should be added to the tutorial for sure, thanks for the suggestion. The default behaviour is actually saving it to `$pwd/.singularity`, which is also default behaviour of `singularity...

Hmmmm, seems like most steps went fine, except the connection with dockerhub: ``` Error: FATAL: Unable to handle docker://dynverse/ti_slingshot:v1.0.3 uri: failed to get SHA of docker://dynverse/ti_slingshot:v1.0.3: pinging docker registry returned:...

Hi! Could you try to run this using `model

Hi @friedue This might be related to a memory issue. We do use sparse matrices internally now, but slingshot cannot handle these... Looking at the dimensions of your data, slingshot...

This is a bug somewhere in the preprocessing of scanpy. I guess somewhere genes are removed before the `n_top_genes` are selected, meaning that less than `n_top_genes` are available and thus...

`dynverse/ti_paga:v0.9.9.05` now has a parameter `filter_features`. If FALSE, this will skip the filtering. As far as I know, this is only necessary when there are < 100 features, such as...