On Wed, Mar 20, 2013 at 3:51 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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

Some years later, this question has been resurrected as

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