Troubleshooting

Installing on Python \(\geq\) 3.13 on Windows

User reports / CI testing have suggested that up to version 1.1.1, installing SCEPTR on Python \(\geq\) 3.13 on Windows results in an error. This issue is fixed from version 1.2.0 onwards. If Windows users notice any persisting problems despite using the latest version of SCEPTR, please submit an issue on the GitHub repository to notify the maintainers.

Mus musculus TR genes / alleles not properly recognised as functional

This was a known bug with old versions of the libtcrlm dependency. This has now been fixed thanks to a contribution from @celinebalaa (thank you!). If you are still having this issue, please make sure your Python environment has libtcrlm updated to version 1.1.2 or newer, and if the issue is persisting please open an issue on the GitHub repository.

Error from git when installing from source (versions \(\leq\) 1.1.0)

A recent security update to git has resulted in some difficulties cloning repositories that rely on git-lfs. This can result in an error message with a message along the lines of:

$ fatal: active `post-checkout` hook found during `git clone`

If this happens, you can temporarily set the GIT_CLONE_PROTECTION_ACTIVE environment variable to false by prepending GIT_CLONE_PROTECTION_ACTIVE=false before the install command like below:

$ GIT_CLONE_PROTECTION_ACTIVE=false pip install git+https://github.com/yutanagano/sceptr.git@<VERSION_TAG>

This is a known issue for git version 2.45.1 and is fixed from version 2.45.2.