ipyrad doesn't look for ipcluster in the right place

[DBrusson]

When trying to use ipyrad, it fails at the begining because it can't find ipcluster:

$ ipyrad -p params-Rj02.txt -s 1234567 -f

 -------------------------------------------------------------
  ipyrad [v.0.9.92]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
Error launching ipcluster for parallelization:
([Errno 2] No such file or directory: '/usr/local/python/python-3.11.4/bin/ipcluster')

The problem is ipcluster is in $HOME/.local/bin/ipcluster. PATH, PYTHONPACKAGES and PYTHONPATH are correctly set, so why is it looking in the wrong place ?

[isaacovercast]

It's looking in /usr/local for the ipcluster launcher, which indicates that the conda env isn't correctly configured in your path. Can you show echo $PATH?

You say ipcluster is installed in $HOME/.local/bin, is this where conda is installed or are you using an alternate configuration (not a conda environment)?

It might just be easier to rm -rf .ipython and then remove your minconda install and reinstall miniconda from scratch, if this is something youre comfortable with it usually fixes most weird install problems.

[DBrusson]

I'm not using conda. But I found the bug. It's in ipyrad/core/Parallel.py, line 27 :

IPCLUSTER_BIN = os.path.join(sys.prefix, "bin", "ipcluster")

It doesn't work if the package are bit in the same location as the python executable, which is the case on our cluster. I did a patch that seems to work (but I'm a total noob in Python, I guess it can be better):

IPCLUSTER_BIN=os.popen('which ipcluster').read().strip()

which ipcluster will locate ipcluster in PATH .read() will store the results in IPCLUSTER_BIN .strip() will remove \n from the result

[isaacovercast]

Ahh, cool, that makes sense. That is a fine solution for your needs, it makes sense. Glad you figured it out!

Thanks for letting me know. Good luck with the rest of the assembly!