Bug Report: LTR Element Identification Fails When Running HiTE via Singularity Container

[Scy-bio]

When running HiTE for Transposable Element (TE) annotation using the provided demo genome via a Singularity container, the LTR identification module produces empty output files. However, when installing and running HiTE in a Conda environment on the same system and with the same input, the LTR identification works as expected and yields the results.
Since the Conda version runs without issue, the problem seems to lie within the container image packaging or runtime configuration.

[spriego]

Hi,

I observed the same issue when running HiTE 3.3.3 container.

It looks like LTRDetector is not compiled inside the container and the LTR detection fails.

Could the developer please confirm and possibly rebuild the container with the compiled LTRDetector binary included?

Thanks a lot !

[SwiftSeal]

Yep also seeing this in the 3.3.3 container

[spriego]

I ended up running the HiTE 3.3.2 container and it works fine.