'/var/log/gigadb/transfer.log': Permission denied

[only1chunts]

Describe the bug
when testing v4.4.0 on staging I get an error when attempting to use the "transfer" script

To Reproduce
Steps to reproduce the behavior:

1. Follow instructions for 1-5 on https://github.com/gigascience/gigadb-website/blob/develop/docs/curators/CURATOR_TOOLS_BASTION.md
2. at point 6, when I run the command as suggested:
   transfer --doi 102621 --sourcePath . --wasabi --apply
3. then I get a permission denied error stating:
   touch: cannot touch '/var/log/gigadb/transfer.log': Permission denied

Expected behavior
Not sure what the expected outcome is, but probably not a permission denied error.

Suggestion
Could it be that to run the transfer script we should be using sudo? If so the instructions need correcting.

[kencho51]

I was able to execute the tool as user lily in my staging:

[lily@ip-10-99-0-77 ~]$ transfer --doi 102480 --sourcePath /share/dropbox/user101/ --wasabi --backup
More details about copying files to Wasabi bucket, please refer to: /var/log/gigadb/transfer.log
More details about copying files to s3 bucket, please refer to: /var/log/gigadb/transfer.log
[lily@ip-10-99-0-77 ~]$ cat /var/log/gigadb/transfer.log
2024/11/20 07:08:55 INFO  : Start copying files from staging to Wasabi
2024/11/20 07:08:58 NOTICE: readme_102480.txt: Skipped update modification time as --dry-run is set (size 3.127Ki)
2024/11/20 07:08:58 NOTICE: analysis_data/Tree_file.txt: Skipped update modification time as --dry-run is set (size 359)
2024/11/20 07:08:58 INFO  : There was nothing to transfer
2024/11/20 07:08:58 NOTICE: 
Transferred:              0 B / 0 B, -, 0 B/s, ETA -
Checks:                 2 / 2, 100%
Elapsed time:         2.4s

2024/11/20 07:08:58 INFO  : Executed: rclone copy --s3-no-check-bucket --s3-profile wasabi-transfer /share/dropbox/user101/ wasabi:gigadb-datasets/staging/pub/10.5524/102001_103000/102480 --dry-run --log-file /var/log/gigadb/transfer.log --log-level INFO --stats-log-level DEBUG >> /var/log/gigadb/transfer.log
2024/11/20 07:08:58 INFO  : Successfully copied files to Wasabi bucket for DOI: 102480
2024/11/20 07:08:58 INFO  : Start copying files from staging to s3
2024/11/20 07:08:58 NOTICE: readme_102480.txt: Skipped update modification time as --dry-run is set (size 3.127Ki)
2024/11/20 07:08:58 NOTICE: analysis_data/Tree_file.txt: Skipped update modification time as --dry-run is set (size 359)
2024/11/20 07:08:58 INFO  : There was nothing to transfer
2024/11/20 07:08:58 NOTICE: 
Transferred:              0 B / 0 B, -, 0 B/s, ETA -
Checks:                 2 / 2, 100%
Elapsed time:         0.4s

2024/11/20 07:08:58 INFO  : Executed: rclone copy --s3-no-check-bucket --s3-profile aws-transfer /share/dropbox/user101/ gigadb-datasetfiles:gigadb-datasetfiles-backup/staging/pub/10.5524/102001_103000/102480 --dry-run --log-file /var/log/gigadb/transfer.log --log-level INFO --stats-log-level DEBUG >> /var/log/gigadb/transfer.log
2024/11/20 07:08:58 INFO  : Successfully copied files to s3 bucket for DOI: 102480
[lily@ip-10-99-0-77 ~]$