Question about GTDBtk about metabolic HOT 6 CLOSED

Hi,
METABOLIC-C will use gtdbtk. I am not sure whether you mean the path of the gtdbtk database or the output folder of gtdbtk run.

from metabolic.

Thank you. I'm referring to the path of the gtdbtk database. Is there a way to specify it along with the run command?

from metabolic.

I breifly looked at gtdbtk, found that it is not easy to set a new path for gtdbtk database instead of the default. We use gtdbtk by using its default settings. Maybe it will be easier to just re-install your gtdbtk.

from metabolic.

Hey @ChaoLab,

I'm sorry I wasn't clearer earlier. According to the installation instructions, one can do the following:

# Set the GTDBTK_DATA_PATH environment variable in the file:
$PATH/metabolic/etc/conda/activate.d

I was wondering, instead of doing the above whether one could do something like the below:

perl METABOLIC-C.pl <input> <output> --database PATH/TO/GTDBtk-database

I'm guessing you don't have that functionality - please let me know if otherwise.

Thank you!

from metabolic.

It seemes one can set gtdbtk database path during installation. While, once after installation, gtdbtk database path is fixed, I could not find an option from gtdbtk to change the path.

from metabolic.

Fair enough - thank you!

from metabolic.