installation with conda into an environment

[mtva0001]

Hi, I try to install medaka but it is not an easy task apparently. I try to install it into an already existing conda environment using: conda install -c conda-forge -c bioconda medaka

But I got this error: UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• medaka -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.5,<3.6.0a0|3.4.|3.7.10|3.7.10|3.6.12|3.7.9|3.6.12|3.6.9|3.6.9|3.6.9|3.6.9|>=3|>=3.6|3.7.*|<3.0.0|>=3.5',build='0_73_pypy|1_73_pypy|3_73_pypy|1_73_pypy|0_73_pypy|5_73_pypy|5_73_pypy|4_73_pypy|2_73_pypy']
• medaka -> python[version='>=3.6,<3.7.0a0']

Your python: python=3.9

Can you make medaka compatible with any version of python?

[cjw85]

Medaka is untested on Python 3.9 and Python 3.10, hence the restriction to Python <= 3.8.

We advise to install medaka into a standalone conda environment.

[mtva0001]

Yes, well, another software (pipeline) requires medaka and I cannot load two environments at the same time (or I don't know how to do that). Any solution for such scenario?

[cjw85]

Most workflow management software like snakemake and nextflow provide the ability to use different software environments for different stages of workflows. I would contact the author of the software pipeline you are using and ask them to set this up.

It is unlikely that tested support for Python 3.9 will come to medaka soon.

[mtva0001]

I downgraded python and still get this error: UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• medaka -> python[version='2.7.|3.5.|3.6.|3.4.|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|3.7.10|3.7.10|3.6.12|3.7.9|3.6.12|3.6.9|3.6.9|3.6.9|3.6.9|>=3|>=3.6|3.7.*|<3.0.0|>=3.5',build='2_73_pypy|5_73_pypy|1_73_pypy|0_73_pypy|5_73_pypy|4_73_pypy|3_73_pypy|1_73_pypy|0_73_pypy']
• medaka -> python[version='>=3.6,<3.7.0a0']

Your python: python=3.8

[cjw85]

As stated above, we recommend that medaka is installed in a standalone virtual or conda environment. Due to the myriad possibilities that may occur otherwise, we cannot support use outside of this setup.

[mtva0001]

Well, I don't have other options if Nanopore doesn't provide a complete pipeline for clustering, consensus creation and making an OTU table finally. Anyway, then I'm forced to use Racon instead.

[cjw85]

Closing this issue. The recommendation remains that medaka should be installed in to an isolated conda or virtual environment, this is easily specified in workflow managers commonly used in bioinformatics.