Trimmomatic wrapper bug

[dpryan79]

Trimmomatic wrapper bug

[pjbriggs]

Hello @dpryan79

Thanks for reporting this issue, I can see there will be a problem when using paths containing spaces.

As you suggest, quoting the arguments in the wrapper shell script would address this problem. However as part of trying to make the tool compatible with Galaxy's conda dependency resolver, I'm planning to drop the shell script completely - the changes are currently in PR #23.

With these changes all file paths should be quoted, so hopefully this problem will go away. However if you are able to review the changes perhaps you can comment if you see any pitfalls.

HTH

Peter

[dpryan79]

👍 Anything that gets away from the shell script should resolve the problem.

[pjbriggs]

Great. I still need to test the changes and push them to the toolsheds, hopefully I'll get a chance this week.

[pjbriggs]

@dpryan79 sorry this took a lot longer to than anticipated due to other commitments, however the conda-compatibility updates have now been finished and pushed to the toolsheds (PR #23).

As part of this the wrapper script has been purged, and the inputs and outputs are now quoted. So hopefully this addresses your issue.

[dpryan79]

+1

…

Sent from my iPhone

On 16 Dec 2016, at 11:53, Peter Briggs ***@***.***> wrote: @dpryan79 sorry this took a lot longer to than anticipated due to other commitments, however the conda-compatibility updates have now been finished and pushed to the toolsheds (PR #23). As part of this the wrapper script has been purged, and the inputs and outputs are now quoted. So hopefully this addresses your issue. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.