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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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BUG: conda activate, conda-unpack, RScript not found. #332

Closed carmensandoval closed 1 year ago

carmensandoval commented 1 year ago

Hi, I just made a fresh clone of the repo and I see this error I had not encountered before: Any ideas why this could be happening? My previous clone did have conda-unpack and conda-activate.

> /path/to/bin/zUMIs/zUMIs.sh -c -y zUMIs_tiny.yaml

Using miniconda environment for zUMIs!
 note: internal executables will be used instead of those specified in the YAML file!

/path/to/bin/zUMIs/zUMIs.sh: line 161: /path/to/bin/zUMIs/zUMIs-env/bin/activate: No such file or directory
/path/to/bin/zUMIs/zUMIs.sh: line 162: conda-unpack: command not found
/path/to/bin/zUMIs/zUMIs.sh: line 171: Rscript: command not found
carmensandoval commented 1 year ago

Resolved by removing the zumis-env directory and running zUMIs.sh with -c option again.

cziegenhain commented 1 year ago

Hi Carmen,

Typical error that happens when the first run after cloning is interruped & the unpacking of the conda environment doesn't complete. But as you say, removing the zumis-env directory and rerunning will fix this.