cory-weller / h5ad-to-seurat

Converting big anndatas!

Note that in my case source myconda is a script within ${PATH} that initializes conda.

Create conversion (anndata) environment

mamba create -p convert 'scanpy' 'anndata'

Create Seurat5 + BPCells environment

mamba create -p bpcells 'r-seurat>=5' 'r-remotes' 'hdf5'
mamba activate bpcells/
Rscript -e 'remotes::install_github("bnprks/BPCells/r")'
mamba deactivate

Submit jobs (takes ~220 GB of memory for my 22 GB h5ad object)

sbatch scripts/split.sh data/04_ad-ftd_anndata_object.h5ad

And after splitting is complete...

sbatch scripts/convert.sh