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Missing sbmlTranslator binary

See original GitHub issue

Hi!

I freshly installed pysb with conda and the sbml importer fails with the following error:

FileNotFoundError: [Errno 2] No such file or directory: '[...]/share/bionetgen/bin/sbmlTranslator': '[...]/share/bionetgen/bin/sbmlTranslator'

Going to that location, the binary is a symbolic link: lrwxrwxrwx 1 [...] share/bionetgen/bin/sbmlTranslator -> ../../../bin/sbmlTranslator which points to miniconda3/bin/sbmlTranslator, which doesn’t exist.

By the way, I’m using pysb.importers.sbml.model_from_biomodels.

Issue Analytics

State:
Created 4 years ago
Comments:5 (4 by maintainers)

Top GitHub Comments

1reaction

alubbockcommented, Sep 9, 2019

Thanks @maurosilber for the report. I’ve created a pull request to improve the error message and documentation here: #460.

1reaction

ortega2247commented, Sep 9, 2019

Hi. PySB uses atomizer to translate sbml models into bionetgen and then translates bionetgen to the pysb format. To get your code working you just need to install atomizer from conda:

conda install -c alubbock atomizer

Maybe we should add this to the documentation @alubbock ??

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