On Dec 4, 2012, at 11:57 AM, Josh Nielsen wrote:

> Great. I'll give those ideas a shot to see if it gets me anywhere. 
> 
> P.S. You referenced in the email that I linked to a fix in the next release 
> of Galaxy. Is that out yet or still in development?

The fix was in the September 7, 2012 distribution release, so it'd be a good 
idea to make sure your release is at least that new.

--nate

> 
> -Josh
> 
> On Tue, Dec 4, 2012 at 10:44 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> On Dec 4, 2012, at 11:23 AM, Josh Nielsen wrote:
> 
> > Hi Nate,
> >
> > Thanks for the reply. No I hadn't thought to add anything to 
> > /etc/init.d/galaxy itself. It is a short enough script that I can paste it 
> > below. What would I need to do to edit it with umask settings?
> >
> > Also I should note, changing the umask in the PAM files actually did change 
> > the default permissions for the galaxy user when I did an "su - galaxy" in 
> > a bash shell and then created or 'touch'-ed any files (which you could 
> > logically expect). But for some reason it didn't seem to make a difference 
> > with the directories created in that tmp/ directory even though the galaxy 
> > user was given ownership. That made me wonder if something was going on 
> > internal to Galaxy, or something else, that was overwriting/ignoring the 
> > system umask settings (which actually work fine in a shell environment as 
> > the user itself). Maybe I'll look into that ACL stuff Paul mentioned.
> 
> Paul's suggestions are worth checking in to.  I'd be interested in knowing 
> what the POSIX permissions are on /tmp itself, and what the ACLs are, if any.
> 
> Those temporary files are created by creating a temporary directory using 
> Python's tempfile.mkdtemp(), which creates them with a mode of 700, which is 
> then masked by the current umask.  The change I added in the email you 
> referenced in your original post changes the directory to mode 0777 masked by 
> the umask (after it's created).
> 
> Depending on how the pieces used in RHEL's startup() shell function handle 
> the environment, you may be able to set it on the line above `daemon ...` 
> inside the 'start)' branch of the case statement.  If that doesn't work, you 
> may need to get more creative and do something like:
> 
>     daemon --user $GALAXY_USER "umask 027; ${GALAXY_RUN} --daemon 
> --pid-file=${GALAXY_PID}"
> 
> Alternatively, you can set it inside /home/galaxy/galaxy-dist/run.sh, since 
> this startup script uses run.sh.
> 
> --nate
> 
> > Here is my /etc/init.d/galaxy script:
> >
> > ------------------------
> > . /etc/rc.d/init.d/functions
> >
> > GALAXY_USER=galaxy
> > GALAXY_DIST_HOME=/home/galaxy/galaxy-dist
> > GALAXY_RUN="${GALAXY_DIST_HOME}/run.sh"
> > GALAXY_PID="${GALAXY_DIST_HOME}/paster.pid"
> >
> > case "$1" in
> >         start)
> >                           echo -n "Starting galaxy services: "
> >                           daemon --user $GALAXY_USER "${GALAXY_RUN} 
> > --daemon --pid-file=${GALAXY_PID}"
> >                           touch /var/lock/subsys/galaxy
> >         ;;
> >         stop)
> >                           echo -n "Shutting down galaxy services: "
> >                           daemon --user $GALAXY_USER "${GALAXY_RUN} 
> > --stop-daemon"
> >                           rm -f /var/lock/subsys/galaxy
> >         ;;
> >         status)
> >                           daemon --user galaxy "${GALAXY_RUN} --status"
> >         ;;
> >         restart)
> >                           $0 stop; $0 start
> >         ;;
> >         reload)
> >                           $0 stop; $0 start
> >         ;;
> >         *)
> >                           echo "Usage: galaxy 
> > {start|stop|status|reload|restart}"
> >         ;;
> > esac
> > --------------
> >
> > Thanks!
> > Josh
> >
> > On Tue, Dec 4, 2012 at 9:56 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> > On Dec 4, 2012, at 10:52 AM, Josh Nielsen wrote:
> >
> > > 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?
> >
> > Hi Josh,
> >
> > Thanks for doing such extensive tests.  Have you tried setting the umask in 
> > the init script itself?
> >
> > --nate
> >
> > >
> > > Thanks,
> > > Josh Nielsen
> >
> >
> 
> 


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