Issue with file permissions of uploaded files
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
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.de>wrote:
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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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 Toedling <j.toedling@imb-mainz.de>wrote:
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
______________________________**_____________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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 Toedling<j.toedling@imb-mainz.de>wrote:
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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participants (3)
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Joern Toedling -
Kanwei Li -
Nate Coraor