Open abretaud opened 1 year ago
Try running this before running funannotate:
export FUNANNOTATE_DB=/path/to/funannotate/db
Alternatively, you can add a couple of files in your conda environment so the FUNANNOTATE_DB
variable is set automatically when loaded.
The first one sets FUNANNOTATE_DB
when you activate the environment:
touch /path/to/miniconda3/envs/funannotate/etc/conda/activate.d/funannotate.sh
and add the command to the activate.d/funannotate.sh
:
export FUNANNOTATE_DB=/path/to/funannotate/db
And a second file so conda can unload the variable, when you deactivate the environment:
touch /path/to/miniconda3/envs/funannotate/etc/conda/deactivate.d/funannotate.sh
and add this to the deactivate.d/funannotate.sh
:
unset FUNANNOTATE_DB
Yep I know I can do it, but when running funannotate annotate --database xxxx
, funannotate sets the FUNANNOTATE_DB internally before calling other scripts. I would expect it to do the same when it calls iprscan2annotations.py
I'm getting the same error. I agree with @abretaud that it is very odd that funannotate expects an environment variable $FUNANNOTATE_DB
to be set when there is a command line variable --database
which should override that.
This sounds like a bug, it can be fixed I just need to find some time....
Are you using the latest release? yes, 1.8.15 from conda
Describe the bug Running
funannotate annotate
command with an interproscan.xml input file, I get this error:Apparently this line expects a FUNANNOTATE_DB which does not exist in my case (I used the --database option of
funannotate annotate
)