Hello all,
I am having issues downloading HTML files from Galaxy the same as is described in this email chain:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-August/010965.html
I am getting the error "(13)Permission denied: xsendfile: cannot open file: /basedir/galaxy_data/database/tmp/tmp8iEccn/library_download.zip" which is indeed a basic filesystem permissions issue. The problem is that the permissions created for that directory and every directory created in tmp/ look like this:
drwx------+ 2 galaxy galaxy 3 Dec 4 09:23 tmp8iEccn
And I have placed the Apache user in the galaxy group, but as you can see no group permissions ever get set by Galaxy on the directories that it creates (it is getting a 700 permissions setting).
As Nate Coraor suggested in the message linked to above, I have tried altering the default umask but I ran into issues with getting non-existant results. I use "sudo service galaxy start" as the galaxy user each time to start the server and a "ps -ef | grep galaxy" confirms that Galaxy is running as the galaxy user. Since I use sudo though I changed the sudoers file to include:
root ALL=(ALL) ALL galaxy ALL=(ALL) ALL Defaults umask_override Defaults umask = 0002
This changed absolutely nothing. Then I started looking deeper into the PAM configuration and added a umask directive to /etc/pam.d/sudo (and also tried it in password-auth-ac and system-auth-ac) like this: "session optional pam_umask.so umask=0002". Still nothing changed in the permissions in tmp/ when I tried to download an HTML file: no group permissions were set. Then I dug deeper still and saw that sometimes if setting the mask in /etc/pam.d/ config files is not enough that you can try to set a system-wide mask in /etc/login.defs (following the suggestion here: http://stackoverflow.com/questions/10220531/how-to-set-system-wide-umask). Still no dice. I've pretty much exhausted my know-how in this department. Any other suggestions of how to fix this or where the correct place to set the umask is?
Thanks, Josh Nielsen