On Thu, Mar 13, 2014 at 5:32 PM, Wang, Xiaofei xfwang@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!