Closed martenson closed 7 years ago
Quoting @natefoo on galaxy-dev http://dev.list.galaxyproject.org/Running-jobs-as-real-user-and-extra-file-path-td4586608.html#a4598557
On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor nate@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
I don't know how things stand now, but agree file_path vs extra_file_path would be good to address in the IUC guidelines.
So any tool outputs that use the extra files directory should use the output's 'files_path' attribute.
From Nate's statement above, I understand that tools should be using $output.files_path
. Is that correct? ping @natefoo
This thread is newer http://dev.list.galaxyproject.org/snpeff-tool-for-Galaxy-extra-files-path-td4665799.html and includes a writeup of my attempt to sort this all out in https://bitbucket.org/galaxy/galaxy-central/pull-requests/532/fix-for-datatypes-consuming-output-extra/diff.
The tl;dr is that the @jmchilton endorsed approach is:
$input.extra_files_path for inputs and $output.files_path for outputs
Thanks @jmchilton - I was puzzled not to be able to find anything more recent on this in my email archive.
I believe this has been clarified, so can it be closed?
Is this, or can we add this as text to the standards?
Let's add something based on John's recommendation to the docs under http://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html
Touched at https://github.com/galaxyproject/galaxy/pull/3918
It is my impression these are the same thing and Galaxy supports both. What is the recommended standard?
ping @galaxy-iuc/iuc