These are chat archives for dereneaton/ipyrad

19th
Jul 2018
Isaac Overcast
@isaacovercast
Jul 19 2018 16:25
@tommydevitt Hm, i might have an idea. Look at the structure directions for this recent workshop I gave: https://radcamp.github.io/AF-Biota/05_STRUCTURE_API.html
Look at the section titled: Configure HPC environment for ipyparallel (THIS IS VERY IMPORTANT)
Isaac Overcast
@isaacovercast
Jul 19 2018 16:33
echo "export QT_QPA_PLATFORM=offscreen" >> ~/.profile
That's the most important part. It's dying on the headless cluster.
tommydevitt
@tommydevitt
Jul 19 2018 16:37

@isaacovercast Thanks, I'll try it. Unfortunately I updated conda and now am getting import errors when I try to import the ipyrad analysis toolkit:
ImportError: cannot import name demultiplex

I uninstalled and reinstalled everything and ipyrad works, but I can't import the library via the notebook. Had the same problem before, but was able to fix it using Mariana's code. Not this time it seems. When I try to import ipyrad by hand as you suggested before I get a segmentation fault.

Isaac Overcast
@isaacovercast
Jul 19 2018 17:45
Are you running the notebook inside the ipyrad source directory? What directory are you running the notebook in?
tommydevitt
@tommydevitt
Jul 19 2018 17:49
Running the notebook from a different directory (/work/02745/tdevitt/lonestar/Eurycea/JA17735) than the ipyrad source directory. They have to be in the same directory?