default settings.yaml lacks 'log-dir' specification

BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline

GNU General Public License v3.0

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default settings.yaml lacks 'log-dir' specification #112

Closed smoe closed 2 years ago

smoe commented 2 years ago

It remains unclear if the log dir of gridengine is meant or local directory where to place all the standard output files.

pigx-rnaseq -s settings.yaml sample_sheet.csv
Commencing snakemake run submission to cluster
Traceback (most recent call last):
  File "/usr/bin/pigx-rnaseq", line 525, in <module>
    if config['execution']['cluster']['log-dir']:
KeyError: 'log-dir'

borauyar commented 2 years ago

Yes, I have also encountered this. @rekado this was introduced recently under pigx-common package: in pigx-common/common/pigx-runner.in. This should be only when executing on the cluster, right?

smoe commented 2 years ago

Yes, it only surfaces with an enabled cluster (I installed gridengine and thought I should give it a try, failed because of a missing sme environment, though).

borauyar commented 2 years ago

This issue was listed before (https://github.com/BIMSBbioinfo/pigx_rnaseq/issues/101). I am closing this one.