diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md index ea1c787c..b6e47ca4 100644 --- a/docs/troubleshooting.md +++ b/docs/troubleshooting.md @@ -1,5 +1,25 @@ # Troubleshooting + +## Installation via conda - perl-clone missing + +When installing AGAT via Conda you might encounter the following error message: + +``` +LibMambaUnsatisfiableError: Encountered problems while solving: + - nothing provides perl-clone needed by agat-1.4.2-pl5321hdfd78af_0 +Could not solve for environment specs +The following package could not be installed +|- agat 1.4.2** is not installable because it requires + |- perl-clone, which does not exist (perhaps a missing channel). +``` + +This issue occurs when using a computer with an ARM64 processor architecture, such as an Apple computer with an M1, M2, M3, or similar processor. +The perl-clone package requires platform-specific (compiled) code, and a compatible compilation has not yet been produced for this Conda recipe. + +Hopefully, this will become available in the future. +In the meantime, the alternatives are to use the AGAT container via [Docker](https://github.com/NBISweden/AGAT?tab=readme-ov-file#using-docker) or [Singularity](https://github.com/NBISweden/AGAT?tab=readme-ov-file#using-singularity). + ## AGAT throws features out, because the feature type is not yet taken into account Feature types (primary_tag) handled by AGAT are defined within `feature_levels.yaml` file. Most common features are already defined in this file. If you encounter GFF/GTF files with feature types not accepted, AGAT will inform you and throw the features out. To keep those feature you must inform AGAT how to handle them: First access the feature_levels.yaml files by running: