Persistent error with `FROGS_preprocess` tool (line 77 of tool_script.sh)

Galaxy
1

Hi,

Since yesterday afternoon, the FROGS_preprocess tool (v4.2.0+galaxy0) has been consistently failing, even with datasets that had previously been processed successfully.

The error shown is:
/shared/ifbstor1/galaxy/datasets2/jobs/006/032/6032632/tool_script.sh: line 77: [: missing `]'

The “Command line” field is empty, and the "Tool Standard Outpoot" is also empty. This seems to be related to an error in the tool’s script.
The issue persists today with new test jobs.

Today’s job ID: 72b671e5dcbb4d11
Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/4.2.0+galaxy0

Thank you very much for any help you could bring me,
Olivia

2

The tool has recently been updated to version 4.2.0. However, it appears that a bug may have been introduced in this release, particularly when used with your dataset.

I report the issue to the developers. Syntax error in FROGS_preprocess v4.2.0+galaxy0 missing `]` in wrapper · Issue #78 · geraldinepascal/FROGS · GitHub
In the meantime, you can continue using a previous version (e.g., 4.1.0), which remains compatible with your data and is working as expected.
Thomas