On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor <n...@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

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