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Christensen-Lab-Dartmouth / PyMethylProcess

Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.
https://christensen-lab-dartmouth.github.io/PyMethylProcess/
MIT License
35 stars 8 forks source link

download_clinical throws error #11

Open shucon opened 4 years ago

shucon commented 4 years ago

I'm trying to download the clinical information on a Docker Machine using pymethyl-preprocess download_clinical and I'm getting the following error:

Screenshot from 2020-11-01 18-53-41

PS: It would be great if someone can upload the clinical data for TCGA. So that I can continue working in the meantime. :smiley:

jlevy44 commented 4 years ago

clinical_info.csv.zip It's been a while, but let me know if this is what you're looking for!

jlevy44 commented 4 years ago

I'm assuming that you're following this?: https://github.com/Christensen-Lab-Dartmouth/PyMethylProcess/blob/master/example_scripts/TCGA.md

shucon commented 4 years ago

I'm assuming that you're following this?: https://github.com/Christensen-Lab-Dartmouth/PyMethylProcess/blob/master/example_scripts/TCGA.md

@jlevy44 Yes, I'm following that. Although, now I have the clinical info I was able to continue with the rest of the pipeline without any major hiccups.

So if it's not a priority issue, you can keep it on hold.

Thanks a lot. :smiley:

jlevy44 commented 3 years ago

Thanks! Sorry this function seems to have been problematic as of late. Definitely on my to-do list!