Hi all, I'm wondering if someone who has downloads working through apache (using xsendfile) has encountered this error when downloading HTML files: (13)Permission denied: xsendfile: cannot open file: /galaxy_data/production/tmp/tmpN0ydYt/library_download.zip The output from ls -lZ /galaxy_data/production/tmp is: ... drwx------. galaxy galaxy unconfined_u:object_r:httpd_sys_content_t:s0 tmpN0ydYt ... The output from ls-lZ /galaxy_data/production/tmp/tmpN0ydYt/ is: -rw-rw-r--. galaxy galaxy unconfined_u:object_r:httpd_sys_content_t:s0 library_download.zip It's not a SElinux issue (if I sudo setenforce 0, the problem persists).. It seems it's a regular permissions issue (user apache is running httpd and does not permission to enter the tmpN0ydYt). Since galaxy creates these files with these permissions I don't know how to fix this issue. I'm also wondering why the HTML datasets are in the tmp folder not the files folder? Here's my apache config: <VirtualHost *:80> ServerName ________________ RewriteEngine on #RewriteOptions Inherit #RewriteLog "/etc/httpd/logs/rewrite_log" #RewriteLogLevel 5 RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /usr/local/galaxy/production/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /usr/local/galaxy/production/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /usr/local/galaxy/production/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /usr/local/galaxy/production/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /usr/local/galaxy/production/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] <Location "/galaxy"> order allow,deny allow from all # Compress all uncompressed content SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary # Send files through Apache XSendFile on XSendFilePath /galaxy_data </Location> <Location "/galaxy/static"> # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault "access plus 6 hours" </Location> </VirtualHost> Is there something wrong with it? Or have I missed something in universe.wsgi? Cheers, Julian
On Jul 17, 2012, at 3:16 PM, Julian Pradinuk wrote:
Hi all,
I'm wondering if someone who has downloads working through apache (using xsendfile) has encountered this error when downloading HTML files:
(13)Permission denied: xsendfile: cannot open file: /galaxy_data/production/tmp/tmpN0ydYt/library_download.zip
The output from ls -lZ /galaxy_data/production/tmp is: ... drwx------. galaxy galaxy unconfined_u:object_r:httpd_sys_content_t:s0 tmpN0ydYt ... The output from ls-lZ /galaxy_data/production/tmp/tmpN0ydYt/ is: -rw-rw-r--. galaxy galaxy unconfined_u:object_r:httpd_sys_content_t:s0 library_download.zip
Hi Julian, This should be fixed in 7588:068a043f6bb1, which will be in our next stable release. You'll need to make sure that your Galaxy server process starts under a umask(2) that will give group and/or other permissions. If you allow group-only access, your Galaxy user will need to start with a group that your Apache server is a member of. --nate
It's not a SElinux issue (if I sudo setenforce 0, the problem persists).. It seems it's a regular permissions issue (user apache is running httpd and does not permission to enter the tmpN0ydYt). Since galaxy creates these files with these permissions I don't know how to fix this issue. I'm also wondering why the HTML datasets are in the tmp folder not the files folder?
Here's my apache config: <VirtualHost *:80> ServerName ________________ RewriteEngine on #RewriteOptions Inherit #RewriteLog "/etc/httpd/logs/rewrite_log" #RewriteLogLevel 5 RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /usr/local/galaxy/production/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /usr/local/galaxy/production/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /usr/local/galaxy/production/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /usr/local/galaxy/production/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /usr/local/galaxy/production/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
<Location "/galaxy"> order allow,deny allow from all
# Compress all uncompressed content SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
# Send files through Apache XSendFile on XSendFilePath /galaxy_data </Location>
<Location "/galaxy/static"> # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault "access plus 6 hours" </Location> </VirtualHost>
Is there something wrong with it? Or have I missed something in universe.wsgi?
Cheers,
Julian
___________________________________________________________ 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:
participants (2)
-
Julian Pradinuk -
Nate Coraor