Error during installation: Conda fails to resolve dependencies

[mptrsen]

Installation with dependencies from Conda according to the instructions fails at the Pkg.instantiate() step. Long error output here. Perhaps the issue is that the distutils package is deprecated and the submodule sysconfig wasn't found:

$ mamba create -p conda/patchwork -c bioconda -c conda-forge diamond julia
$ mamba activate conda/patchwork/
$ git clone https://github.com/fethalen/patchwork
$ cd patchwork/
$ julia --project=. -e 'import Pkg; Pkg.instantiate()'
[...long list of dependencies being downloaded...]
ERROR: Error building `PyCall`: 
<string>:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'distutils.sysconfig'
[...]

[ClaraKoehne]

Hello! I can't reproduce the error on my system. But in the long error output, it seems like you have no system-wide python installation? I'm not sure how to solve this. However, it seems like something else is broken in the conda installation of julia anyways; for the latest julia version (1.8.2), I am missing some certificate files when installing with conda. The alternative would be to not use a conda environment but instead download julia and diamond like so:

wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.2-linux-x86_64.tar.gz
tar -xzf julia-1.8.2-linux-x86_64.tar.gz

(julia version 1.8.2 for Linux)

wget http://github.com/bbuchfink/diamond/releases/download/v2.0.13/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz

(diamond version 2.0.13 for Linux) Make sure that both programs are in your $PATH variable so that you can call them from the terminal. I should add that Patchwork's main branch might be broken right now, but that's an issue I'm currently solving.

[ClaraKoehne]

The main branch should work again now, just so you know.