Question: Galaxy Installation fails
0
gravatar for mranjan1
17 months ago by
mranjan10
United States
mranjan10 wrote:

Hi there!

My galaxy installation fails and displays this error. Can anyone help? The first time I installed Galaxy, it was successful and I could open it on port 8080. However, after multiple failed attempts to log in as an administrator. I deleted the galaxy folder and downloaded a new copy. I load the Python 2.7 module before I try installation but it still crashes.

Any feedback would be much appreciated.

Thanks!

Exception: Traceback (most recent call last): File "/software/python/2.7.13/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/software/python/2.7.13/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/software/python/2.7.13/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install **kwargs File "/software/python/2.7.13/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/software/python/2.7.13/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/software/python/2.7.13/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_files clobber(source, lib_dir, True) File "/software/python/2.7.13/lib/python2.7/site-packages/pip/wheel.py", line 323, in clobber shutil.copyfile(srcfile, destfile) File "/software/python/2.7.13/lib/python2.7/shutil.py", line 83, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 13] Permission denied: '/software/python/2.7.13/lib/python2.7/site-packages/psyco_full.py'

galaxy • 624 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by mranjan10

What are the permissions in /software/python/2.7.13/lib/python2.7/site-packages?

ADD REPLYlink written 17 months ago by Devon Ryan1.9k

I just started working with Linux yesterday so this might be hard for me to find out. Let me try..

ADD REPLYlink written 17 months ago by mranjan10
0
gravatar for Dannon Baker
17 months ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

When you say you load the python 2.7 module prior to installation, what do you mean exactly? This looks like Galaxy's pip is trying to install extra dependencies to a directory which the user you are running as does not have write access to, which is a problem.

ADD COMMENTlink written 17 months ago by Dannon Baker3.7k

In my first attempt, I got an error message saying Galaxy works with Python 2.7. Following that, I tried module load python/2.7.13 (which our bioinformatics core has preinstalled) and then did sh run.sh. Galaxy installed and was available at 127.0.0.1:8080

Since I deleted galaxy and tried to reinstall it, it would stop with the error given above.

ADD REPLYlink written 17 months ago by mranjan10
0
gravatar for mranjan1
17 months ago by
mranjan10
United States
mranjan10 wrote:

I realized that every time I change the port, galaxy installs but it doesn't run twice on the same port. So, if I want to launch Galaxy again, I have to edit the port in galaxy.ini

In every instance when galaxy installed and I could open it on the browser, not a single time did it let me log into my account and returned invalid user/password.

Does that give you any clue as to what am I doing wrong?

ADD COMMENTlink written 17 months ago by mranjan10

Can you look at the Galaxy log files? It sounds like you might be starting several Galaxy servers successfully, but just have not registered the account that you are trying to log in as.

ADD REPLYlink written 17 months ago by Dannon Baker3.7k

Where can I find the galaxy log file?

According to the Galaxy manual, I add my usegalaxy.org login to admin_users and remove the # from the line. Still, no success logging in.

I was wondering if there was a way to terminate all servers that may be running (if that's what happening). That brings me to another question, how do I terminate a galaxy instance safely?

ADD REPLYlink written 17 months ago by mranjan10
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