Problem with setting environment variable $BIOBAKERY_WORKFLOWS_DATABASES

Infrastructure and utilities bioBakery workflows
1

Hi

I have been trying to install the environment variable BIOBAKERY WORKFLOWS with pip (Installing the workflows with pip · biobakery/biobakery_workflows Wiki · GitHub) and then BIOBAKERY WORKFLOWS DATABASES using $ biobakery_workflows_databases --install --wmgx. After solving for many errors, I have now hit the wall in the form of “setting environment variable $BIOBAKERY_WORKFLOWS_DATABASES”

As suggested in “Installing the workflows with pip” I have installed the workflows in a static environment: install_workflows. However, due to the disk space restrains from the univ management, the databases need to be installed at a custom location (in my case, it is /scratch/users/nus/saxena/miniconda3/envs/biobakery/opt/biobakery_workflows_databases). Now, for that I have set the environment variable by specifying
“export BIOBAKERY_WORKFLOWS_DATABASES=/scratch/users/nus/saxena/miniconda3/envs/biobakery/opt/biobakery_workflows_databases” in .bashrc file. However, I am still getting the error “A custom install location was selected. Please set the environment variable $BIOBAKERY_WORKFLOWS_DATABASES to the install location.”

May I know if there is any specific way of setting the environmental variable?

Requesting your help

Regards
Gourvendu

Exp_var
Exp_var1259×817 36.9 KB

Env_Var_err
Env_Var_err1325×824 67.1 KB

2

Hello,
Have you found solution to this problem? I have the same question, using biokabery as a conda environment and have to install databases in an other location than the default. Do you put the export PATH: $BIOBAKERY_WORKFLOWS_DATABASES in your .bashrc?

thanks

3

Hello, Thank you for the detailed post. Sorry for any confusion. The software will always print the message about setting an environment variable when a custom location is selected. The software does not check if the environment variable is set.

Thank you,
Lauren