[galaxy-dev] Problems linking Data inside Galaxy

[Gaueko Erge]

Hi,

I have followed, carefully, the instructions posted in:
http://wiki.galaxyproject.org/Admin/Data%20Integration

Yet, despite my best efforts when I get, say all exons from hg19 build and
try to their fetch sequences, galaxy tells me that the sequences for hg19
are not there

I find this surprising because I have downloaded:

rsync://datacache.g2.bx.psu.edu/indexes/
rsync://hgdownload.cse.ucsc.edu/gbdb/
rsync://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/bigZips

databases and added the correct paths to the 'alignseq.loc' file

Any ideas will be appreciated

Thanks

--G
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[galaxy-dev] Socket error starting galaxy

[Gaueko Erge]

Hi,
On a fresh galaxy installation the server start fine when it looks at port
8080, but as soon as I change to port 80 I get the following error
I think that is due to permissions since I have my galaxy inside a non-root
galaxy user directory
Any ideas on the best way to solve this would be appreciated
Thanks
--G

Starting server in PID 8799.
Traceback (most recent call last):
  File "./scripts/paster.py", line 34, in 
command.run()
  File
"/usr/local/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 84, in run
invoke(command, command_name, options, args[1:])
  File
"/usr/local/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 123, in invoke
exit_code = runner.run(args)
  File
"/usr/local/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
line 218, in run
result = self.command()
  File
"/usr/local/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
line 303, in command
serve()
  File
"/usr/local/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
line 287, in serve
server(app)
  File
"/usr/local/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
line 151, in server_wrapper
**context.local_conf)
  File
"/usr/local/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py",
line 57, in fix_call
val = callable(*args, **kw)
  File
"/usr/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1314, in server_runner
serve(wsgi_app, **kwargs)
  File
"/usr/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1264, in serve
threadpool_options=threadpool_options)
  File
"/usr/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1114, in __init__
RequestHandlerClass, ssl_context)
  File
"/usr/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1094, in __init__
RequestHandlerClass, ssl_context)
  File
"/usr/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 328, in __init__
HTTPServer.__init__(self, server_address, RequestHandlerClass)
  File "/usr/lib/python2.7/SocketServer.py", line 408, in __init__
self.server_bind()
  File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
SocketServer.TCPServer.server_bind(self)
  File "/usr/lib/python2.7/SocketServer.py", line 419, in server_bind
self.socket.bind(self.server_address)
  File "/usr/lib/python2.7/socket.py", line 224, in meth
return getattr(self._sock,name)(*args)
socket.error: [Errno 13] Permission denied
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