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 <jmchil...@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 > > 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 > 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 > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ >
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