Alex,

This is definitely an issue, but it is not currently high priority for the 
Galaxy team. 

We expect to move the Velvet wrappers to the tool shed in the near future, and 
from there others can enhance the wrappers as needed. In the meantime, 
community contributions to the Galaxy code base, including existing tool 
wrappers, are most welcome.

Best,
J.


On Oct 8, 2012, at 7:53 PM, Oleksandr Moskalenko wrote:

> Velveth wrapper passes the location of the 
> database/files/xxx/dataset_yyy_files to the velveth as an argument. Same 
> paths are put into the output html file. This method can't work anymore when 
> jobs are submitted under real user names as a real user doesn't have write 
> permissions outside of the exernal_chown_script, so the velveth wrapper is 
> broken for all installations using real user id jobs at this time.
> 
> Regards,
> 
> Alex
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