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GEO-BON / bon-in-a-box-pipeline-engine

Pipeline engine that can run R, Julia, Python and shell scripts seamlessly.
GNU General Public License v3.0
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fallback if env not present while yml file is. #137

Closed jmlord closed 1 month ago

jmlord commented 1 month ago

closes #130

glaroc commented 1 month ago

Getting an error when running loadFromSTAC

There was an error in previous run: running again.
Activating existing conda environment data__loadFromStac
mv: cannot stat '/conda-env-yml/data__loadFromStac.2.yml': No such file or directory
FAILED
Error: script returned non-zero value
Error: output.json file not found
Runner: biab-runner-conda version 2024-09-19 14:14
jmlord commented 1 month ago

Getting an error when running loadFromSTAC

There was an error in previous run: running again.
Activating existing conda environment data__loadFromStac
mv: cannot stat '/conda-env-yml/data__loadFromStac.2.yml': No such file or directory
FAILED
Error: script returned non-zero value
Error: output.json file not found
Runner: biab-runner-conda version 2024-09-19 14:14

I can't see how this happens...

                                    if [ -f "$condaEnvFile.2.yml" ]; then
                                        if cmp -s $condaEnvFile.yml $condaEnvFile.2.yml; then
                                            echo "Activating existing conda environment $condaEnvName"
                                        else
                                            echo "Updating existing conda environment $condaEnvName"
                                            mamba env update -f $condaEnvFile.2.yml ; assertSuccess
                                        fi

                                        mv $condaEnvFile.2.yml $condaEnvFile.yml ; assertSuccess
                                    fi

it checks for the file right before the mv command. Are you sure you are running the right version of the code?

glaroc commented 1 month ago

Stopping and restarting the server fixed the issue.