setup problem

[sittnerr]

Hey, I started the pipeline by installing the environment and entering the first lines of code without a problem, however, when I enter:

for fol in [folder_path_base, folder_path_analysis, folder_path_ilastik, folder_path_ome, folder_path_cp, folder_path_histocat, folder_path_cp_input]: if not fol.exists(): fol.mkdir(parents=True)

I get the error message PermissionError: [Errno13] Permission denied: '.../analysis'

this '.../analysis' looks like its from defining folder_path_base earlier in the script I was able to use the mkdir command to create the folders, but the part if not fol.exists(): ... creates the problem;

in addition, when trying to import the url from the example dataset, I have a problem with the following command:

import urllib.request fol_example = folders_path_inputs[0] fol_example.mkdir(exist_ok=True) urls = [('20170905_Fluidigmworkshopfinal_SEAJa.zip', 'https://www.dropbox.com/s/awyq9p7n7dexgyt/20170905_Fluidigmworkshopfinal_SEAJa.zip?dl=1') , ('20170906_FluidigmONfinal_SE.zip', 'https://www.dropbox.com/s/0pdt1ke4b07v7zd/20170906_FluidigmONfinal_SE.zip?dl=1')]

for fn, url in urls: fn = fol_example / fn if not fn.exists(): urllib.request.urlretrieve(url, fn)

leaving for_example.mkdir(exist_ok=True) in line 3 out allows me to run the command, but still nothing is downloaded

Could you help me?

[nilseling]

Hey @sittnerr,

it looks like you don't have write access to the working directory. Please change the access rights or chose a different working directory. Best,

Nils

[sittnerr]

Hey @nilseling ,

Thank you for the quick response! I tried changing the access using chmod but it didn't work, what code should I use to allow access?

Best, Richard

[nilseling]

Hmm, hard to tell since I don't know your system. The easiest would be to work in your home directory cd ~ for testing purposes.

[sittnerr]

that's my script till now, no added data myself, just trying to set it up

[sittnerr]

I am working in the home directory already - is there any data you need to understand the problem?

[nilseling]

Are you executing the script from your home directory? So in your terminal (not jupyter) you execute the following commands:

cd ~
git clone https://github.com/BodenmillerGroup/ImcSegmentationPipeline.git

cd ImcSegmentationPipeline

conda activate ImcSegmentationPipeline

jupyter notebook

[sittnerr]

Thank you! Got it!!!

[nilseling]

No worries!