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

On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor nate@bx.psu.edu wrote:

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On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote:

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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 https://github.com/galaxy-iuc/standards/issues/40

Peter