Tools downloading but not working

usegalaxy.org support
1

Hi there,

I had issues with downloading tools, but since installing mercurial, they will install but when I came to use one of the tools I had installed, the output generated was not correct. When I clicked on one of the output files this information was shown … “0 bytes” and “/bin/sh: /Volumes/My: No such file or directory”

When I look in the error log it says
[Errno 2] No such file or directory: ‘/Volumes/My Book/Galaxy/galaxy/tool-data/sift_db.loc’
[Errno 2] No such file or directory: ‘/Volumes/My Book/Galaxy/galaxy/tool-data/add_scores.loc’
[Errno 2] No such file or directory: ‘/Volumes/My Book/Galaxy/galaxy/tool-data/codingSnps.loc’

but I have recent gone into data-tool folder and duplicated the sample versions of these files and renamed the copy removing the “sample” part of the name. So I’m not sure why it is still saying this.

Any help would be greatly appreciated!!

thanks

2

Lauren,

Having wrapped a couple of tools throughout my career, I’m pretty sure that this is caused by the input dataset paths in the tool XML definition not being escaped with single quotes, so the code thinks the input files are separated by spaces like so:

/Volumes/My + Book/Galaxy and so on.

To get that issue fixed, you would need to contact the tool author or maintainer to update the XML definition, and when that has been completed, install the new version of the tool.