It looks like this was a problem for awhile but isn't anymore on main
https://trello.com/c/yFeXvhUg.

It doesn't look like there has been any changes to the bowtie2 wrapper
since it was migrated to the tool shed so I am not sure why it isn't
working for you?

As an admin can you open a successful bowtie2 dataset and see what the
standard error and standard output are saved as - maybe copying them
into pastebin or gist. It might help illuminate the problem.

-John

On Mon, Oct 27, 2014 at 4:31 AM, Elizabeth Chia <elchia@gmail.com> wrote:
> Dear all
>
>
> Usually the alignment statistics from bowtie2 will be printed to the stderr
> file, however, on the local instance, the stderr file is empty after
> alignment. It still does the alignment, but the statistics are not printed
> out.
>
> This is my hg summary:
> parent: 13802:f7dd0060c296 latest_2014.06.02
>  Merged in dannon/galaxy-central-prmaker/stable (pull request #404)
> branch: stable
> commit: 288 modified, 357 added, 18 unknown (new branch head)
> update: 27 new changesets (update)
>
> Will updating to the latest version help?
>
> Or are there any patches available?
>
> Thanks.
>
>
> Regards
> liz
>

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