Re: [galaxy-dev] ⇝ IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'
Hi Luciano, I also ran into the same error after upgrading to the latest build. I found that the following files were owned by root. Not sure how they got changed. galaxyTools/galaxy-central/database/compiled_templates/tool_form.mako.py galaxyTools/galaxy-central/database/compiled_templates/tool_form.mako.pyc After chown and chgrp the files to galaxy, things now are working ok for me again. Give that a try. Cheers, Dave On Mon, May 14, 2012 at 10:12 AM, Luciano Cosme wrote: > Hi, > Yes. It is same user and the only used of this system. > Thank you. > > > > On Fri, May 11, 2012 at 1:33 PM, Nate Coraor wrote: > >> >> On May 10, 2012, at 6:59 PM, Luciano Cosme wrote: >> >> > >> > Hi Everyone, >> >I was just using my local galaxy instance. I closed it up (from >> terminal), open IGV to look at some genes, then I restarted it from the >> terminal and when I tried to access it I got the error message below. I >> just don't know what happened in these few minutes. Any suggestion how to >> fix it? >> > Thank you. >> > >> > Luciano >> > >> > URL: http://127.0.0.1:8080/ >> > >> ... >> > module = imp.load_source(self.module_id, path, open(path, 'rb')) >> > IOError: [Errno 13] Permission denied: >> u'/home/koala2/galaxy-central/database/compiled_templates/ >> base_panels.mako.py' >> >> Hi Luciano, >> >> Could you verify that you started Galaxy as the same user both times? >> >> --nate >> >> > >> > ___ >> > 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/ >> >> > > > > ___ > 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/ > ___ 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/
Re: [galaxy-dev] ? IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'
I have seen this error many times (for various mako.py files) and it is often either when the user running it has insufficient privileges or the file permissions on a folder (could be several directories upstream) or a file have changed in some way. If you do a 'ps -ef | grep python' do you see the paster.py process running with your expected user? Do you use sudo to elevate the privileges when you run it? I use a 'galaxy' user but I execute run.sh (which I have created a service script for in /etc/init.d) with sudo while logged in as galaxy. Also you might want to do an 'ls -l' in the compiled_templates/ directory and look at the file permissions and file ownership. -Josh ___ 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/
Re: [galaxy-dev] ⇝ IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'
Hi, Yes. It is same user and the only used of this system. Thank you. On Fri, May 11, 2012 at 1:33 PM, Nate Coraor wrote: > > On May 10, 2012, at 6:59 PM, Luciano Cosme wrote: > > > > > Hi Everyone, > >I was just using my local galaxy instance. I closed it up (from > terminal), open IGV to look at some genes, then I restarted it from the > terminal and when I tried to access it I got the error message below. I > just don't know what happened in these few minutes. Any suggestion how to > fix it? > > Thank you. > > > > Luciano > > > > URL: http://127.0.0.1:8080/ > > > ... > > module = imp.load_source(self.module_id, path, open(path, 'rb')) > > IOError: [Errno 13] Permission denied: > u'/home/koala2/galaxy-central/database/compiled_templates/ > base_panels.mako.py' > > Hi Luciano, > > Could you verify that you started Galaxy as the same user both times? > > --nate > > > > > ___ > > 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/ > > ___ 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/
Re: [galaxy-dev] ⇝ IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'
On May 10, 2012, at 6:59 PM, Luciano Cosme wrote: > > Hi Everyone, >I was just using my local galaxy instance. I closed it up (from terminal), > open IGV to look at some genes, then I restarted it from the terminal and > when I tried to access it I got the error message below. I just don't know > what happened in these few minutes. Any suggestion how to fix it? > Thank you. > > Luciano > > URL: http://127.0.0.1:8080/ > ... > module = imp.load_source(self.module_id, path, open(path, 'rb')) > IOError: [Errno 13] Permission denied: > u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py' Hi Luciano, Could you verify that you started Galaxy as the same user both times? --nate > > ___ > 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/ ___ 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/
