cantinilab/momix-notebook

momix-notebook's Issues

jupyter-notebook segmentation fault

Hi,

I was able to install the conda environment momix following the readme instructions, but now, trying to run jupyter-notebook I get "segmentation fault".

My OS is MacOS Ventura 13.5.1
The python version installed on Momix is 3.6.15
and I can't get the jupyter-notebook version due to segfault.

Could you please help me resolve this issue?

MOFA error

When I run momix-notebook/scripts/Comparison in simulated data.ipynb, ## Running the comparisons. I got the error message as shown below. Could the error be related to depreciated MOFA v1?

Warning message in createMOFAobject(omics):
“View names are not specified in the data, renaming them to: view_1, view_2, view_3
”
Creating MOFA object from list of matrices,
please make sure that samples are columns and features are rows...

Checking data options...

Checking training options...

Checking model options...

[1] "No output file provided, using a temporary file..."
Error in py_module_import(module, convert = convert): ModuleNotFoundError: No module named 'mofa'
Traceback:

1. runfactorization(simul_folder, paste0("omics", 1:3, ".txt"),
   . num.clusters, sep = "\t", filtering = "none")
2. runMOFA(MOFAobject)
3. import("mofa")
4. py_module_import(module, convert = convert)

Data files closed or moved?

Hello I am trying to run the jDA analysis however am hitting an error when trying to retrieve the single cell data files:

curl: (28) Failed to connect to acgt.cs.tau.ac.il port 80 after 127929 ms: Connection timed out
unzip: cannot find or open aml.zip, aml.zip.zip or aml.zip.ZIP.
rm: cannot remove ‘aml.zip’: No such file or directory

Pb with installation of GenomeInfoDbData in the conda environment

(Windows 10, using Ubuntu 16.10 in WSL)

I had problems during the creation of the momix conda environment. Everything seemed to run fine, but when I tried executing one of the notebooks in the momix environment it complained about a missing package "GenomeInfoDbData". Indeed it seemed like it was not correctly installed in R.

I had to execute the following command to install it properly (as suggested on the anaconda website) :
conda install -c bioconda/label/gcc7 bioconductor-genomeinfodbdata
This seemed to solve the problem for my setup.

Cheers,
Céline

Probelm with environment setup

Hello, we want to use your environment and the notebooks to test the performance of other jDR Methods.
Unfortunately we were not able to get the environment created with the current miniconda version and the command you provided in the README. Is there possibly a conflict with the python 3.11.4 of the current miniconda version? On my Windows PC i got the following result:

Unreadable Notebook: /home/zly/code/Multi-omics/momix-notebook/scripts/Comparison_in_cancer.ipynb FileNotFoundError(2, 'No such file or directory')

Unreadable Notebook: /home/zly/code/Multi-omics/momix-notebook/scripts/Comparison_in_cancer.ipynb FileNotFoundError(2, 'No such file or directory')