Database path

[madscort]

Database path

[jakobnissen]

We have hit the exact same issue now and can't easily run CheckM2 for this reason.
Our current workaround is that each individual user in our cluster downloads and installs CheckM2 independently, but that's not a great solution.

[madscort]

I apparently missed that the path can be set by setting the environmental variable CHECKM2DB using:
export CHECKM2DB="path/to/database"

[chklovski]

Thanks, I've added a description of CHECKM2DB variable. Release 1.0.1 now also has a --database_path option for checkm2 predict.

[maxibor]

Ehy @chklovski and @dparks1134 ,
This looks like it is the same issue from Checkm1 (see Ecogenomics/CheckM#326) which has a simple fix: allow to save the configuration file somewhere else.

I believe something like this should do the trick (with an extra CLI flag to get the config path):

CheckM2/checkm2/defaultValues.py

Lines 5 to 9 in e563159

	class DefaultValues():
	"""Default values for filenames and common constants."""
	DATA_PATH = os.path.join(os.path.dirname(__file__), 'data')
	MODEL_PATH = os.path.join(os.path.dirname(__file__), 'models')
	VERSION_PATH = os.path.join(os.path.dirname(__file__), 'version')

class DefaultValues():
     """Default values for filenames and common constants.""" 
    def __init__(self, default_dir=None):
           if default_dir:
                self.default_dir = default_dir
           else:
                 self.default_dir = os.path.dirname(__file__)
     DATA_PATH =  os.path.join(self.default_dir , 'data') 
     MODEL_PATH = os.path.join(self.default_dir , 'models') 
     VERSION_PATH = os.path.join(self.default_dir , 'version') 

[nick-youngblut]

I apparently missed that the path can be set by setting the environmental variable CHECKM2DB using:
export CHECKM2DB="path/to/database"

It would be very helpful to add this info to https://github.com/chklovski/CheckM2#database

Better yet: adding --database-path to checkm2 predict would be awesome