On Wed, Mar 20, 2013 at 3:51 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor <nate(a)bx.psu.edu>
> 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
> in the config file's 'file_path' option and should be used when providing
> 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.
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:
If I'm using a single Linux/Unix galaxy user this doens't matter does it?