I Running run.sh as root helped me get rid of the permission denied errors. After modifying the apache and galaxy config files, restart the apache web server then run the run.sh as root $ sudo su root $ source galaxy_env/bin/activate $ sh galaxy_dist/run.sh Hope this helps Lucie ----------------------------------------------------------- Lucie Hutchins Scientific Software Engineer The Jackson Laboratory Email: lucie.hutchins@jax.og web: harlequin.jax.org Phone: 1-207-288-6764 ________________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Yu Wang [yu.wang@wzw.tum.de] Sent: Tuesday, April 12, 2011 4:13 PM To: diehl@immunbio.mpg.de Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Apache configuration problem? hi, sarah, sorry for the confusion. I did change those lines with my own directories. And the files are readable for others. Regards, Yu Yu Wang Office: Department of Plant Science Center for Life and Food Sciences Weihenstephan Technical University Munich Lehrstuhl für Pflanzenzüchtung Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Technische Universität München Room 026, Emil-Ramann-Str. 4 (old: Am Hochanger 4) Tel: ++49 8161 71-4139 Lab: Lehrstuhl für Genomorientierte Bioinformatik Maximus-von-Imhof-Forum 3. Room OG-L 09 Tel: ++49 8161 71-2132 yu.wang@wzw.tum.de D-85354 Freising Germany ___________________________________________________________ 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: http://lists.bx.psu.edu/