On Thu, Mar 13, 2014 at 5:32 PM, Wang, Xiaofei <xfw...@ku.edu> wrote:
> Hi Folks,
> I figured out the problem of tool dependencies successfully. The
> installation status is installed for all tool sheds. The tools are also
> shown on left tool panel. But, I got problems when I used the tool sheds to
> analyze data.
> For example,
> When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open
> file '~/softwares/shed_tools/
> /galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory
> When I checked the ~/.../galaxy folder, there are four *.xml files.
> Then, I copied the four files from ~/.../script folder. Now, this tool
> works. But, I don't think this is a right way to figure out this because I
> also got similar problem (I think they are similar) when I used other tool
> sheds as below. So, I am guessing it might be a problem with my configure
> file (universe_wsgi.ini). Could anybody tell me why and how to figure it
I am responsible for answering the first part of your error message, It is
my mistake that I have to place the right path in the tool configuration
file (xml). This will be fixed soon and update the repository to a new
Vipin | Rätsch Lab
> BWA wrapper error:
> when I used the BWA wrapper for Illunina,
> An error occurred with this dataset:
> Could not determine BWA version
> Error indexing reference sequence. /bin/sh: bwa: command not found
> I referred to this link to try to figure out the problem
> But, I think I need more details about the mentioned bwa binaries and path.
> When I used the snpEff, the error is:
> Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar
> In fact, the snpEff.jar is located at
> Could you give me some ideas?
> Thank you so much!
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