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sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
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Conda package support for Python 3.7+ #312

Open zmunro opened 3 years ago

zmunro commented 3 years ago

Is there support for Python3.7+? I am trying to install ariba into my conda environment following the guide on this page. I tried using the first command there which is conda install -c bioconda ariba but that gave me this error:

UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions

So I tried using the second command there which is conda install -c bioconda/label/cf201901 ariba and that gave me this error:

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - ariba -> python[version='3.4.*|3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']

Your python: python==3.7.4=h265db76_1

I'm not sure what the issue with the first command is but the second command seems to return an error saying that ariba does not support any Python version greater than 3.7.0a0. Given that we are at Python3.9.1, it would be great to get support for Python3.7.

rpetit3 commented 3 years ago

Hi @zmunro ,

I just saw this, I think this is more of a conda issue. I wonder if creating a new environment would have solved your problem.

conda create -n ariba -c conda-forge -c bioconda ariba
valery-shap commented 3 years ago

Hello, I've tried

conda create -n ariba -c conda-forge -c bioconda ariba

and I have an error while Ariba test out

` the output didn't match this regular expression: ".bowtie2.version (.*)$"

Something wrong with at least one dependency. Please see the above error message(s) ARIBA version: 2.14.6

External dependencies: bowtie2 ERROR /home/miniconda3/envs/ariba/bin/bowtie2 cdhit 4.8.1 /home/miniconda3/envs/ariba/bin/cd-hit-est nucmer 3.1 /home/miniconda3/envs/ariba/bin/nucmer

External dependencies OK: False `

version of bowtie2 with conda installation: bowtie2 bioconda/linux-64::bowtie2-2.3.5.1-py36he513fc3_0

What version of bowtie2 should be?

Best regards, Valery

ddomman commented 3 years ago

@valery-shap

I ran into this bowtie error after upgrading my ariba conda environment. After doing some digging, it seems this is a problem with the tbb package. Installing a downgraded version solves the problem.

conda install tbb=2020.2

KasperThystrup commented 2 years ago

I can confirm the tbb package issue. Related: https://github.com/conda-forge/tbb-feedstock/issues/75