Thank you for responding.
Not too sure why I can't see your link unfortunately, but did you mean
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?
On Mon, Nov 3, 2014 at 6:59 AM, John Chilton <jmchil...@gmail.com> wrote:
> It looks like this was a problem for awhile but isn't anymore on main
> 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.
> On Mon, Oct 27, 2014 at 4:31 AM, Elizabeth Chia <elc...@gmail.com> wrote:
> > Dear all
> > Usually the alignment statistics from bowtie2 will be printed to the
> > file, however, on the local instance, the stderr file is empty after
> > alignment. It still does the alignment, but the statistics are not
> > 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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