Hello all,

I am having issues downloading HTML files from Galaxy the same as is
described in this email chain:


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:
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?

Josh Nielsen
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