Hi Joern,

Would it be easier to just chmod the directories to reflect the new user?

-K

On Wed, Aug 24, 2011 at 4:42 AM, Joern Toedling j.toedling@imb-mainz.dewrote:

Hi all,

we have our own Galaxy server running under Nginx. Recently we changed the 'user' of Nginx in the Nginx configuration file from 'galaxy' to a more general 'www' since we plan to use Nginx for other purposes as well.

Now the "Get data -> Upload file" does not work any longer because of file permissions. Files are uploaded correctly to a directory /local/data/galaxy_tmp/upload_**store/ but then are owned by the 'www' user and read-writeable by this other only. Thus, the Galaxy user 'galaxy' cannot open them, cannot determine the file type and the whole "Upload file" process fails.

How can I set the file permissions of uploaded files? Do I need to enter a matching 'umask' in some Galaxy configuration or in some Nginx configuration file. Any links to where to set such a umask would be greatly appreciated.

Thanks, Joern

-- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511

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Thanks Nate,

putting the "upload_store_access" directive into the nginx.conf indeed did the trick.

Joern

On 08/24/2011 07:45 PM, Nate Coraor wrote:

You can also use the 'upload_store_access' option to the nginx upload module to make the files readable:

 http://www.grid.net.ru/nginx/upload.en.html

--nate

Kanwei Li wrote:

...

Hi Joern,

Would it be easier to just chmod the directories to reflect the new user?

-K

On Wed, Aug 24, 2011 at 4:42 AM, Joern Toedlingj.toedling@imb-mainz.dewrote:

...

Hi all,

we have our own Galaxy server running under Nginx. Recently we changed the 'user' of Nginx in the Nginx configuration file from 'galaxy' to a more general 'www' since we plan to use Nginx for other purposes as well.

Now the "Get data -> Upload file" does not work any longer because of file permissions. Files are uploaded correctly to a directory /local/data/galaxy_tmp/upload_**store/ but then are owned by the 'www' user and read-writeable by this other only. Thus, the Galaxy user 'galaxy' cannot open them, cannot determine the file type and the whole "Upload file" process fails.

How can I set the file permissions of uploaded files? Do I need to enter a matching 'umask' in some Galaxy configuration or in some Nginx configuration file. Any links to where to set such a umask would be greatly appreciated.

Thanks, Joern

-- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511

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