Re: [galaxy-dev] upload file not functioning in local installation galaxy

2013-08-19 Thread Yinan Wan 
Hi Hans-Rudolf,

Thanks for your reply.  But do you have any idea what might be related with
this proxy issue? What is required to open/set for galaxy to run? Or do
you might share your experience of how you solve the problem?

Thanks,
Yinan


On Mon, Aug 19, 2013 at 3:16 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:

 Hi Yinan

 It might be unrelated, but we had a similar issue. The problem was due to
 the proxy settings of our server.


 Regards, Hans-Rudolf


 On 08/16/2013 08:23 PM, Yinan Wan wrote:

 Hi,

 I have installed galaxy on our local server, when I was trying to upload
 data from:
 Get Data - Upload File - choose file.  It is not uploading at all; but
 it works fine when using the URL option.  I wonder do you have any
 suggestions about this problem?

 The output from the command line is pasted below:
 
 128.118.200.158 - - [15/Aug/2013:14:15:41 -0400] GET
 /api/histories/**5969b1f7201f12ae/contents?ids=**f09437b8822035f7
 HTTP/1.1
 200 - 
 http://128.118.201.68:8080/**historyhttp://128.118.201.68:8080/history
 Mozilla/5.0 (Macintosh;
 Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
 Chrome/28.0.1500.95 Safari/537.36
 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] GET
 /api/histories/**5969b1f7201f12ae HTTP/1.1 200 -
 http://128.118.201.68:8080/**historyhttp://128.118.201.68:8080/history
 Mozilla/5.0 (Macintosh; Intel Mac
 OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
 Safari/537.36
 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] GET
 /api/histories/**5969b1f7201f12ae/contents?ids=**f09437b8822035f7
 HTTP/1.1
 200 - 
 http://128.118.201.68:8080/**historyhttp://128.118.201.68:8080/history
 Mozilla/5.0 (Macintosh;
 Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
 Chrome/28.0.1500.95 Safari/537.36
 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] GET /api/users/current
 HTTP/1.1 200 - http://128.118.201.68:8080/; Mozilla/5.0 (Macintosh;
 Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko)
 Chrome/28.0.1500.95 Safari/537.36
 128.118.200.158 - - [15/Aug/2013:14:16:49 -0400] GET
 /tool_runner?tool_id=upload1 HTTP/1.1 200 -
 http://128.118.201.68:8080/; Mozilla/5.0 (Macintosh; Intel Mac OS X
 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
 Safari/537.36
 128.118.200.158 - - [15/Aug/2013:14:17:03 -0400] POST
 /tool_runner/upload_async_**create HTTP/1.1 200 -
 http://128.118.201.68:8080/; Mozilla/5.0 (Macintosh; Intel Mac OS X
 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
 Safari/537.36
 128.118.200.158 - - [15/Aug/2013:14:17:04 -0400] GET
 /tool_runner/upload_async_**message HTTP/1.1 200 -
 http://128.118.201.68:8080/; Mozilla/5.0 (Macintosh; Intel Mac OS X
 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
 Safari/537.36
 128.118.200.158 - - [15/Aug/2013:14:17:08 -0400] GET /history HTTP/1.1
 200 - http://128.118.201.68:8080/; Mozilla/5.0 (Macintosh; Intel Mac
 OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95
 Safari/537.36
 ==

   Thanks,
 Yinan


 --
 Yinan Wan, graduate student
 Bioinformatics and Genomics program
 Huck Institutes of Life Sciences
 the Pennsylvania State University


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-- 
Yinan Wan, graduate student
Bioinformatics and Genomics program
Huck Institutes of Life Sciences
the Pennsylvania State University
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[galaxy-dev] galaxy local installation

2013-04-08 Thread Yinan Wan 
Hi,

I was trying to install the galaxy on my laptop and run into the following
error

Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is
almost certainly a bug in the egg distribution.
Dependency ssh requires pycrypto=2.1,!=2.4
Traceback (most recent call last):
  File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
  File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 345, in resolve
egg.resolve()
  File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
  File build/bdist.linux-i686/egg/pkg_resources.py, line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14
(/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg),
Requirement.parse('pycrypto=2.1,!=2.4'))
Fetch failed.

Because I have numpy installed which seems to be conflict to galaxy, so I
was install with virtual python environment (virtualenv), and also tried
the protection environment provided in the galaxy instruction page (
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer),
and both came across the same error as indicated above.

Some information you may be interested:
(GalaxyENV)yinan@Macbook galaxy-dist$ python -V
Python 2.7.3
(GalaxyENV)yinan@Macbook galaxy-dist$ python scripts/get_platforms.py
macosx-10.7-x86_64-ucs2

It will be great if you can help me out.

Thanks,
Yinan

-- 
Yinan Wan, graduate student
Bioinformatics and Genomics program
Huck Institutes of Life Sciences
the Pennsylvania State University
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