Closed humanpaingeneticslab closed 1 year ago
This is a known problem. Please see PR #149. Did you create a conda env using the latest polyfun.yml
?
Thanks John!
I guess you can close my issue.
We did a quick google search and we didn’t find the link below (PR #149)… already nicely documented :-)
On another note, the script that generates the 2,700 jobs still pulls stuff from the old broad URL; I couldn’t find in the polyfun project where that URL comes from, that despite I could locate the new address in compute_ldscores_from_ld.py:
UKBB_LD_URL = 'https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD’
Have a nice day, Marc.
On Apr 14, 2023, at 09:31, John Blischak @.***> wrote:
This is a known problem. Please see PR #149. Did you create a conda env using the latest polyfun.yml?
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We did a quick google search and we didn’t find the link below (PR #149)… already nicely documented :-)
No worries. Installation is tricky. Please try installing the conda env as below, and then let us know if you still get any installation-related errors.
mamba env create --file polyfun.yml
conda activate polyfun
On another note, the script that generates the 2,700 jobs still pulls stuff from the old broad URL
Could you please open a new Issue to report this problem? The more information you provide (line of the file that uses the old URL; example code to reproduce the error), the easier it will be to potentially fix
@humanpaingeneticslab I'm closing the issue for now, please reopen if needed. I also just updated the file that points to the UKBB LD matrices, so hopefully that problem is resolved as well.
Quick update: finemapper.py
can now be run with rpy2 >= 3.5.9 (#156)
Thanks John!
On Apr 25, 2023, at 10:19, John Blischak @.***> wrote: Quick update: finemapper.py can now be run with rpy2 >= 3.5.9 (#156)
Installed a fresh version of polyfun yesterday, and the test_polyfun.py script would fail 1/2 way through.
That's when using rpy2 version 3.5.10.
Reverting to version 3.5.8 solved the problem. \o/