Dear John Thank you for responding. Not too sure why I can't see your link unfortunately, but did you mean this? http://dev.list.galaxyproject.org/bowtie-wrapper-td4658698.html I've tried modifying the command but doesn't seem to work either. And I can't use the wrapper too? I've just updated galaxy as well but doesn't fix it. Any ideas? Many thanks! Liz On Mon, Nov 3, 2014 at 6:59 AM, John Chilton <jmchilton@gmail.com> wrote:

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

...

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

On Mon, Oct 27, 2014 at 4:31 AM, Elizabeth Chia <elchia@gmail.com> wrote: 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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