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biobakery / biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
http://huttenhower.sph.harvard.edu/biobakery_workflows
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Problem with setting environment variable $BIOBAKERY_WORKFLOWS_DATABASES #15

Closed gssin20 closed 3 years ago

gssin20 commented 3 years ago

Hi

I have been trying to install the environment variable BIOBAKERY WORKFLOWS with pip (https://github.com/biobakery/biobakery_workflows/wiki/Installing-the-workflows-with-pip) and then BIOBAKERY WORKFLOWS DATABASES using $ biobakery_workflows_databases --install --wmgx. Afetr 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."

Requesting your help

Regards Gourvendu

Env_Var_err Exp_var

github-actions[bot] commented 3 years ago

Thank you for creating this issue. We currently field issues through our bioBakery Discourse Support Forum. If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.

ljmciver commented 3 years ago

Hi @gssin20 , Thank you for the detailed issue. The script always prints that warning message when a custom location is selected. The script does not first check to see if the environment variable BIOBAKERY_WORKFLOWS_DATABASES is set. If you have set that variable then please ignore the warning message. Sorry that message was confusing. Please post if you have any other issues.

Thank you, Lauren

github-actions[bot] commented 3 years ago

Thank you for creating this issue. We currently field issues through our bioBakery Discourse Support Forum. If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.