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steineggerlab / ufcg

UFCG: Universal Fungal Core Genes
https://ufcg.steineggerlab.com
GNU General Public License v3.0
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How to resolve warning "Failed to detect environment path" and error "AUGUSTUS-PPX config file is absent or improperly formatted." #16

Closed Changwanseo closed 11 months ago

Changwanseo commented 1 year ago

In conda installation, UFCG requires ufcg -t download to finish installation.

However, current error message

"Failed to detect environment path. --ppxcfg, --seqpath, and --modelpath options should be specified." "ERROR! Block profile model directory is incomplete."

is difficult for users to figure out needs of ufcg -t download

I suggest to add messages such as these

If this is your first time using UFCG, use "ufcg -t download config If you haven't downloaded model, use "ufcg -t download minimum" or "ufcg -t download full"

endixk commented 1 year ago

Please run ufcg download -t minimum if you encounter the following warning and error from profile module after the first installation. 

Failed to detect environment path. --ppxcfg, --seqpath, and --modelpath options should be specified.
ERROR! AUGUSTUS-PPX config file is absent or improperly formatted.

These messages may appear again after updating the conda package into the newest version, even if you've been using the previous version of the pipeline. In such cases, running ufcg download -t minimum will resolve the issue as well, however, will occupy unnecessary disk space by downloading another set of databases.

This will be handled by the next update, along with adding better description to the warning messages.

endixk commented 11 months ago

From release v1.0.5, the profiling modules will prompt warning and automatically download resources for their initial run.