conda install incompatibilities

[jannafierst]

Hi, I get these incompatibilities and a failed installation - how can I get around this? Thanks!

warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE Could not solve for environment specs The following packages are incompatible └─ nanocaller is installable with the potential options ├─ nanocaller [2.0.0|2.1.0|2.1.1|2.1.2] would require │ └─ python >=3.6,<3.7 , which can be installed; ├─ nanocaller 2.1.2 would require │ └─ whatshap >=1.0 with the potential options │ ├─ whatshap [1.4|1.6|1.7|2.0|2.1] would require │ │ └─ python >=3.10,<3.11.0a0 , which can be installed; │ ├─ whatshap [1.0|1.1|...|1.7] would require │ │ └─ python >=3.7,<3.8.0a0 , which can be installed; │ ├─ whatshap [1.0|1.1|...|2.1] would require │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ ├─ whatshap [1.1|1.2.1|...|2.1] would require │ │ └─ python >=3.9,<3.10.0a0 , which can be installed; │ └─ whatshap [1.0|1.1|1.2.1|1.3] would require │ └─ python >=3.6,<3.7.0a0 , which can be installed; ├─ nanocaller [3.0.0|3.0.1|3.1.0|3.2.0] would require │ └─ python >=3.8,<3.9 , which can be installed; └─ nanocaller [3.2.0|3.3.0|3.4.0|3.4.1] would require └─ whatshap >=1.4 , which can be installed (as previously explained).

[AstraBert]

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

[kaichop]

Thank you very much for offering a solution!