On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
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
Is this still the case?
I'm guessing this is what Raj was alluding to with the BLAST+ wrapper
for makeblastdb which creates a composite datatype as its output:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013887.html
If I'm using a single Linux/Unix galaxy user this doens't matter does it?
Thanks,
Peter