These are chat archives for dereneaton/ipyrad

1st
Jun 2018
tommydevitt
@tommydevitt
Jun 01 2018 02:52
@isaacovercast If just do python then import ipyrad I get
NameError: name 'python' is not defined
Robin Sleith
@R0cknRobin_twitter
Jun 01 2018 12:15
Hello All,
I am working with ipyrad [v.0.7.23] CLI and have a question about Step 6 checkpoints/substeps. Is there a flag that is needed to ensure that a killed Step 6 will restart from the previous completed checkpoint? For example, clustering across had finished for an assembly but I killed the job in the aligning clusters step. I restarted the assembly calling -s 67 but the assembly just started over at the beginning of Step 6 with concat/shuffle input. Any hints? Thanks! Robin
LinaValencia85
@LinaValencia85
Jun 01 2018 14:22
@isaacovercast yes I am installing it in a cluster. I had done it successfully multiple times in the past, but I proceed to install it yesterday in a new account and I can't. I am assuming there was an update between ipyrad versions that is creating this error? I tried installing llvmlite and I am still getting the same error. "OSError: /lib64/libpthread.so.0: version `GLIBC_2.12' not found "
Edgardo M. Ortiz
@edgardomortiz
Jun 01 2018 16:06

@LinaValencia85 and whoever having trouble in lonestar5:
module unload python2
rm -rf miniconda2 .conda
then download and install latest miniconda:
bash Miniconda2-latest-Linux-x86_64.sh
source ~/.bashrc

then install:
conda install llvmlite=0.22
conda install pyzmq=16
conda install -c ipyrad ipyrad
conda install toytree -c eaton-lab

optional:
conda clean —all

LinaValencia85
@LinaValencia85
Jun 01 2018 16:11
@edgardomortiz @isaacovercast it worked perfectly! Thanks so much!