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!

[odetteg]

I just stumbled on this problem as well. Any ways around it?

[umahsn]

Hi,

The problems could be arising from trying to install NanoCaller in an existing environment that has some python version that is not compatible with NanoCaller dependencies. The best option is to create a new environment to install NanoCaller, ideally by specifying NanoCaller installation during environment creation.

Please try:

Option 1:

 conda create -n ENV_NAME-c bioconda nanocaller
conda activate ENV_NAME
NanoCaller --help

Sometimes conda can take a while to resolve dependencies so it might be faster to install mamba first and then use mamba to install nanocaller.

Option 2:

conda create -n ENV_NAME-c conda-forge mamba
conda activate ENV_NAME
mamba install -c bioconda nanocaller
NanoCaller --help

In either case, it is important to not install other packages before NanoCaller, except for mamba in case of option 2. For example, if you install python before installing NanoCaller, then it is possible that you could end up installing the latest python version 3.13 which may not be compatible with some NanoCaller dependencies. Therefore, it is best to install NanoCaller before other packages.

Lastly, you do not need to install NaoCaller through bioconda. You can just clone NanoCaller github, install dependencies and run NanoCaller by providing full path to the repository. The only thing bioconda installation does is that it adds NanoCaller to the conda environment bin folder in your PATH so that you dont have to use a full path to run NanoCaller. This method is described here: https://github.com/WGLab/NanoCaller/blob/master/docs/Install.md#manual-installation