Running jobs as real user and extra_file_path

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Running jobs as real user and extra_file_path

Louise-Amélie Schmitt
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?

Thanks,
L-A
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Re: Running jobs as real user and extra_file_path

Nate Coraor (nate@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 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

>
> Thanks,
> L-A
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Re: Running jobs as real user and extra_file_path

Peter Cock
On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor <[hidden email]> 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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Re: Running jobs as real user and extra_file_path

Peter Cock
On Wed, Mar 20, 2013 at 3:51 PM, Peter Cock <[hidden email]> wrote:

> On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor <[hidden email]> 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
https://github.com/galaxy-iuc/standards/issues/40

Peter
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