Running example about HMRF

[13954380607]

When I run the HMRF example in Giotto, I met this question, I can't install it in my HPC, could you give me some recommendations? Thank you so much! HMRF spatial genes doHMRF(gobject =visium kidney, expression values ='scaled',spatial network name ='Delaunay full',spatial genes = my spatial genes,K 5.betas =c(0，1，6)，output folder = paste0(hmrf folder,'/',''Spatial genes/SG topgenes k5 scaled')) Warning:this matrix will be converted to a dense and memory intensivebase matrix expression matrix.txt already exists at this location, will beoverwritten spatial genes.txt already exists at this location, will beoverwritten spatial network.txt already exists at this location, will beoverwritten spatial cell locations.txt already exists at this location, will be overwritten[1] "/home/d12373/.1ocal/share/r-miniconda/envs/giotto env/bin/pvthon /home/d12373/,conda/enys/r eny/lib/R/library/Giotto/python/reader2.py -1 \"/home/d12373/data/results/HMRF_results//spatial_genes/sG topgenes_k5 _scaled/spatial cell locations.txt\" -g\"/home/d12373/data/results/HMRF _results//spatial genes/sG topgenes _k5scaled/spatial_genes.txt\" -n \"/home/d12373/data/results/HMRF_results//spatial_genes/sG topgenes_k5_scaled/spatial network.txt\" -e \"/home/d12373/data/results/HMRF results//spatial genes/sG topgenes k5 scaled/exprssion matrix.txt\" -0 \"/home/d12373/data/results/HMRF results//spatial genes/sG topgenes k5 scaled/result..patial.zscore"-atest-k5-b016-t1e-10 -z none -s 100 -i 100"sh:iava:command not found last):Traceback(mostrecent cal1File "/home/d12373/.conda/envs/renv/lib/R/library/Giotto/python/reader2.py",line 122,in if java exists:raise(KeyError(java error_message))KevError: 'Error: iava not found. This function uses a java functionality. Please ensure iava is installedhttps://www.java.com/en/download/

[josschavezf]

@13954380607, you can try using the Giotto singularity image. Here is a tutorial: https://drieslab.github.io/Giotto_website/articles/singularity.html