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?
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
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.
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