conda install incompatibilities about nanocaller HOT 2 OPEN

Dear @jannafierst,

I don't know whether you still need a possible solution to your issue or you worked it out on your own, nevertheless I can propose the workflow I implemented having a similar issue not with my python but with my biopython version.

I work with a Ubuntu 22.04 machine, so consider that the following instructions may not work on your own computer.

I ran

##CREATE A nanocaller ENVIRONEMT
mamba create -p /mnt/c/Users/Astra/envs/nanocaller

##ACTIVATE ENVIRONMENT
mamba activate /mnt/c/Users/Astra/envs/nanocaller

##INSTALL PYTHON
mamba install -c conda-forge -c bioconda -y python=3.10

## INSTALL BIOPYTHON
mamba install -c conda-forge -y biopython

##INSTALL xopen v. 1.2.0
python3 -m pip install xopen==1.2.0

##INSTALL whatshap
mamba install -c conda-forge -c bioconda whatshap

##INSTALL NanoCaller
mamba install -c conda-forge -c bioconda -y nanocaller

##TEST INSTALLATION
NanoCaller -h

I stumbled across several mamba install timeout problems, so you may encounter them: I solved the issues by shutting down and restarting the shell.

Please note that I am nor part of the NanoCaller development team neither of the WGSLab, so this solution might not be optimal, but it worked for me!

Kind regards,
Astra

from nanocaller.

Thank you very much for offering a solution!

from nanocaller.