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/
> toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs
> /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
> out?

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 | R├Ątsch 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
> http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html.
> 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
> ~/softwares/shed_tools/
> toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a
>  Could you give me some ideas?
>  Thank you so much!
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