fragpipe headless issue: ERROR - There is a newer version of MSFragger available [3.6].

[liuxiaoxian]

I'm using FragPipe command mode in a HPC environment. The FragPipe-18.0 works well with MSFragger-3.5 and philosopher-4.4.0. However when I reran a job script that worked previously today, the job failed due to the error "ERROR - There is a newer version of MSFragger available [3.6]". I realize MSFragger has update to 3.6. I wonder if FragPipe command mode requires users keep updating all dependencies to the most recent version?

Thanks!

[fcyu]

For the FragPipe headless mode, yes. In the future release, I will change the error to a warning so that you can still use the old version. But for the FragPipe GUI mode, you can always use the old versions.

Best,

Fengchao

[cpanse]

Using FragPipe 18 and docker, we bypass the issue by disabling the network docker run --rm -it --network none -w $(PWD) ...

[fcyu]

Thanks @cpanse , this is also a good solution.

BTW, we are preparation a docker image for FragPipe. Will upload it to somewhere when it is ready.

Best,

Fengchao

[fcyu]

Hi both,

I made a patch for FragPipe version 18. Please find it from https://www.dropbox.com/sh/52x7mtyobsudge0/AADRLPMvus8CIGbO4v1nMZhZa?dl=0 . You need to replace the fragpipe-18.0.jar in the fragpipe/lib folder (not the fragpipe/bin folder).

Best,

Fengchao

[liuxiaoxian]

Thank you all!

[Munchic]

Hi @fcyu, it seems like in the 19.0 version it still errors when there is a new version, is it possibly to make this a warning instead for 19.0 or 19.1? Thank you.

[fcyu]

Hi @Munchic ,

Yes, you are correct. That bug was found after releasing 19.0, so 19.0 still need a patch. Here it is:#913 (comment)

19.1 should have that fixed.

Best,

Fengchao

[Munchic]

Thank you! So I should update to 19.1 and when next update comes, it will just pop our a warning and everything will still run the same way, right?

[fcyu]

Correct.