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cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
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How should I run sceasy? #40

Open AAA-3 opened 2 years ago

AAA-3 commented 2 years ago

I have run the following code on R with the following errors::

BiocManager::install(c("LoomExperiment", "SingleCellExperiment"))
install.packages('reticulate')
devtools::install_github("cellgeni/sceasy")
library(sceasy)
library(sceasy)
library(reticulate)
use_condaenv('EnvironmentName')
loompy <- reticulate::import('loompy')

Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'loompy'

Detailed traceback: File "/home/ali/R/x86_64-pc-linux-gnu-library/4.0/reticulate/python/rpytools/loader.py", line 44, in _import_hook level=level

sceasy::convertFormat(NueE18.5_noWT2, from="seurat", to="anndata",outFile='NueE18.5_noWT2.h5ad' Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'anndata'

Detailed traceback: File "/home/ali/R/x86_64-pc-linux-gnu-library/4.0/reticulate/python/rpytools/loader.py", line 44, in _import_hook level=level

Am I missing something?

prete commented 2 years ago

@AAA-3 if you're installing it using R, you need to install the python required packages manually. From the terminal do: conda create -n EnvironmentName python=3.6 anndata==0.6.19 scipy==1.2.1 loompy -c bioconda --yes

that should fix all your ModuleNotFoundError