Help and FAQ

This page provides help if you run into problems with refineGEMs.

Help

Known Issues and Bugs

Hint

For bug reports please write issues on the GitHub page or open a discussion here.

Pydantic

Pydantic warning underscore_attrs_are_private has been removed has not - yet - caused any issues. However, the core of the problem (= what causes the warning) has yet to be identified.

FAQ

This site addresses frequently asked questions not addressed in other pages of the refineGEMs documentation.

How do I install refineGEMs?

Please see Installation.

How do I install refineGEMs as a developer?

Please see Installation for developers.

How do I cite refineGEMs?

Please see How to cite.

After restarting my device (MacOS) my conda set-up has the wrong python version. What can I do?

  1. Deactivate all environments including the base environment

  2. Activate your environment for refinegems again

I cannot access python from within my conda environment in my VSCode terminal. What can I do?

Please refer to the solution for After restarting my device (MacOS) my conda set-up has the wrong python version. What can I do?

My pipenv is not locking after f.ex. moving the repository. What can I do?

Try uninstalling pipenv and reinstalling it via pip. Then run pipenv install and it should work again.

How to solve errors caused by pandoc (Development)?

Here is an answer that might help.
If you install pandoc with conda use:
conda install -c conda-forge pandoc

How to solve errors caused by jinja2 (Development)?

Try to switch to version 3.0.3:

pip install jinja2==3.0.3

When do I use lab_strain=True?

If the parameter lab_strain is set to True it is assumed that the input model was created for a strain of an organism for which so far no data is available in any database. To get sufficient information for the knowledge-base stored within the model of the strain the PGAB pipeline described in SPECIMEN should be used before model creation. The resulting FASTA from the PGAB pipeline can then be used als input for CarveMe and is then also required as additional input for polish. In this case the parameter lab_strain should be set to True.