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svalkiers / clusTCR

CDR3 clustering module providing a new method for fast and accurate clustering of large data sets of CDR3 amino acid sequences, and offering functionalities for downstream analysis of clustering results.
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Error installing using conda #39

Open gregoryverghese opened 2 years ago

gregoryverghese commented 2 years ago

Trying to install from svalikiers channel using conda but running into below error. Any ideas?

conda install -c svalkiers clustcr

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \ 
/ 
- 
/ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                          

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions`
MaxVanHoucke commented 2 years ago

Hi there, thanks for reaching out!

The conda package requires some additional channels due to dependencies, the following install command should fix your error: conda install clustcr -c svalkiers -c bioconda -c pytorch -c conda-forge

More information (including how to install the GPU version of ClusTCR) can be found on our docs

gregoryverghese commented 2 years ago

Hi Max, thanks for getting back so quickly.

Having similar problem when I include other channels as well. Any ideas?

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                   

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions
svalkiers commented 2 years ago

Hi Gregory, sorry for this inconvenience.

It looks like there are some version conflicts with other packages. Could you provide a YAML of the environment you are working in?

MaxVanHoucke commented 2 years ago

Coming back to this issue, I encountered very similar output to @gregoryverghese when installing ClusTCR on an M1 mac. When installing dependencies separately (which are listed in the conda/env.yml file), it became clear that faiss did not have a build for this architecture (osx-arm64). After creating a fresh environment, the following command fixed the error. (stackoverflow thread, extra thread)

conda config --env --set subdir osx-64