Re: [galaxy-dev] bowtie2: no stderr output

2014-11-09 Thread Elizabeth Chia
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

Re: [galaxy-dev] bowtie2: no stderr output

2014-11-02 Thread John Chilton
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

[galaxy-dev] bowtie2: no stderr output

2014-10-27 Thread Elizabeth Chia
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