download_clinical throws error

[shucon]

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

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

[jlevy44]

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

[jlevy44]

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

[shucon]

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. 😃

[jlevy44]

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