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? > > Hello, 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 version. regards, 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 > 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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