On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote:

> Hi everyone,
> 
> I just wanted to ask how the extra_file_path is handled in case of job 
> running as the real user since the file_path is only writable by the galaxy 
> user. Any clue?

Hi L-A,

There are actually two dataset attributes for accessing the extra files 
directory, 'files_path' and 'extra_files_path'.

'extra_files_path' always points to the real path under the directory specified 
in the config file's 'file_path' option and should be used when providing a 
dataset's extra files directory as the input to a tool.

'files_path' points at the location that should be written to when used in a 
job so that the job's finish method can find the output files.  This will be 
under the job_working_directory and thus writable by the actual user.  So any 
tool outputs that use the extra files directory should use the output's 
'files_path' attribute.

Sorry for this confusion.  There was talk some time ago about merging both 
attributes to work correctly in all cases, but this was never done.

--nate

> 
> Thanks,
> L-A
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
> http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to