search

sunbeam-labs / sunbeam

A robust, extensible metagenomics pipeline
http://sunbeam.readthedocs.io
167 stars 42 forks source link

Install update all fails with weird paths #420

Closed Ulthran closed 11 months ago

Ulthran commented 1 year ago

Describe the bug Running ./install.sh -e sunbeamX.X.X -u all with sunbeamX.X.X being an existing environment fails. It also seems to be updating the SUNBEAM_VER variable in this weird path where it's doubling the /envs/sunbeam4.0.0 on the end of CONDA_PREFIX.

Output/logs/screenshots

2023-10-20 16:34:39 UTC [     info] Starting Sunbeam installation...
2023-10-20 16:34:39 UTC [     info]     Conda path:   /home/ctbus/miniconda3
2023-10-20 16:34:39 UTC [     info]     Sunbeam src:  /mnt/d/Penn/sunbeam
2023-10-20 16:34:39 UTC [     info]     Sunbeam env:  'sunbeam4.0.0'
2023-10-20 16:34:43 UTC [  warning] Found pre-existing Conda installation in /home/ctbus/anaconda3/envs/sunbeam4.0.0.
2023-10-20 16:34:43 UTC [  warning] Ignoring specified Conda path in favor of existing Conda install.
2023-10-20 16:34:44 UTC [     info] Conda already installed.
2023-10-20 16:34:44 UTC [     info] Creating Sunbeam environment...

CondaValueError: prefix already exists: /home/ctbus/anaconda3/envs/sunbeam4.0.0/envs/sunbeam4.0.0

2023-10-20 16:34:45 UTC [    error] Error in /mnt/d/Penn/sunbeam/install.sh in function debug_capture on line 52
2023-10-20 16:34:47 UTC [     info] Updating SUNBEAM_DIR and SUNBEAM_VER environment variables... 4.0.0-69-g8761678
/home/ctbus/anaconda3/envs/sunbeam4.0.0/envs/sunbeam4.0.0
/home/ctbus/anaconda3/envs/sunbeam4.0.0/envs/sunbeam4.0.0/etc/conda/activate.d/env_vars.sh
2023-10-20 16:34:47 UTC [     info] Environment installed/updated; (re)installing Sunbeam library...
2023-10-20 16:35:01 UTC [     info] Done. Run 'conda activate sunbeam4.0.0' to begin.
2023-10-20 16:35:01 UTC [     info] Optionally, then run 'pytest tests'
2023-10-20 16:35:01 UTC [     info] to make sure the installation is working properly.

Sunbeam version Somewhere between v3.1.1 and v4.1.0

Ulthran commented 11 months ago

Closing this as I've been through multiple iterations of new environments since and haven't encountered the same error. It's likely this was just something I did outside the normal function of sunbeam but if it pops up again I'll reopen this.