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HubertTang / PLASMe

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ResolvePackageNotFound #3

Open abrozzi opened 9 months ago

abrozzi commented 9 months ago 
(base) abrozzi@iMac PLASMe % conda --version
conda 23.9.0
(base) abrozzi@iMac PLASMe %

which is the latest according to https://github.com/conda/conda

But I get this error:

(base) abrozzi@-iMac PLASMe % conda env create -f plasme.yaml                   
Collecting package metadata (repodata.json): \ WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
done
Solving environment: failed

ResolvePackageNotFound: 
  - cudatoolkit=10.2.89
  - libstdcxx-ng=12.2.0
  - _openmp_mutex=4.5
  - libgcc-ng=12.2.0
  - keyutils=1.6.1
  - libnsl=2.0.0

can you help me?

Bests

HubertTang commented 8 months ago

Hi abrozzi,

Sorry for the late reply. The yaml file given now is only suitable for installation on the Linux platform. On other platforms, it may not be installed due to package version issues, especially for the pytorch. You can try to manually install all the required packages via Conda/Mamba. The required package includes the following:

biopython
blast
diamond
numpy
pandas
prodigal
python (version=3.X)
pytorch

The environment should be installable according to the following command:

conda create -n plasme
conda activate plasme
conda install python=3 biopython numpy pandas
conda install -c bioconda blast diamond prodigal
# https://pytorch.org/
conda install pytorch::pytorch torchvision torchaudio -c pytorch

Let me know if you have any other questions about the installation.

Best