Hi Nate,

After scramble,py failed, I ran

$ python ./scripts/scramble.py -e bx_python

and bx_python seems to be built without any problem:

...
writing build/bdist.linux-armv7l/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg' and 
adding 'build/bdist.linux-armv7l/egg' to it
removing 'build/bdist.linux-armv7l/egg' (and everything under it)
scramble(): Copied egg to:
  
/nfs/users/galaxy_dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg


...and I then reran 

$ python ./scripts/scramble.py

 and it shows all eggs already exist. Then I ran 

 $ sh run.sh

to launch Galaxy, without making any change to universe_wsgi.ini. The launch of 
Galaxy failed with the following error message:

...
galaxy.webapps.galaxy.buildapp DEBUG 2013-02-22 15:14:03,077 Enabling 'Request 
ID' middleware
Starting server in PID 19121.
Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
1056, in run
    invoke(command, command_name, options, args[1:])
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
1062, in invoke
    exit_code = runner.run(args)
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 227, 
in run
    result = self.command()
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 677, 
in command
    serve()
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 661, 
in serve
    server(app)
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line 
292, in server_wrapper
    **context.local_conf)
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line 
97, in fix_call
    val = callable(*args, **kw)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
1342, in server_runner
    serve(wsgi_app, **kwargs)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
1291, in serve
    request_queue_size=request_queue_size)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
1134, in __init__
    request_queue_size=request_queue_size)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
1113, in __init__
    request_queue_size=request_queue_size)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-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 98] Address already in use
galaxy.jobs.manager INFO 2013-02-22 15:14:03,134 sending stop signal to worker 
thread
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 job manager queue stopped
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 sending stop signal to worker 
thread
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 job manager stop queue stopped
galaxy.jobs.handler INFO 2013-02-22 15:14:03,136 sending stop signal to worker 
thread
galaxy.jobs.handler INFO 2013-02-22 15:14:03,136 job handler queue stopped
galaxy.jobs.runners.lwr INFO 2013-02-22 15:14:03,136 sending stop signal to 
worker threads
galaxy.jobs.runners.lwr INFO 2013-02-22 15:14:03,137 local job runner stopped
galaxy.jobs.runners.local INFO 2013-02-22 15:14:03,137 sending stop signal to 
worker threads
galaxy.jobs.runners.local INFO 2013-02-22 15:14:03,138 local job runner stopped
galaxy.jobs.handler INFO 2013-02-22 15:14:03,139 sending stop signal to worker 
thread
galaxy.jobs.handler INFO 2013-02-22 15:14:03,139 job handler stop queue stopped
Exception in thread LWRRunner.monitor_thread (most likely raised during 
interpreter shutdown):


I hope you find this information useful. Do you have any idea about what went 
wrong?


Many thanks,
Shun
________________________________________
From: Nate Coraor [n...@bx.psu.edu]
Sent: 21 February 2013 16:56
To: Shun Liang
Cc: James Taylor; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Installing Galaxy on ARM Architecture

On Feb 21, 2013, at 11:47 AM, Shun Liang wrote:

> Sorry just forgot to CC the mailing list.
> ________________________________________
>
> Hi James,
>
> I followed the manual installation instruction on 
> "https://bitbucket.org/james_taylor/bx-python/wiki/HowToInstall";, and 
> surprisingly, bx-python seems to be built on the ARM server without any 
> problem:
>
> Installed 
> /nfs/users/bx-python/lib/python/bx_python-0.7.1-py2.7-linux-armv7l.egg
> Processing dependencies for bx-python==0.7.1
> Finished processing dependencies for bx-python==0.7.1

Hi Shun.

I'm moving this over to galaxy-dev since it's about a local installation.

Galaxy's eggs lib isn't finding the egg you built because Galaxy adds the 
Mercurial revision to the egg version, and then expects the egg to be 
physically located in galaxy-dist/eggs/.  The library will be looking for:

    bx_python-0.7.1_7b95ff194725-py2.7-linux-armv71.egg

If you are able to build it through scramble that would be ideal since it 
handles that naming for you, and there will be other C-Extension eggs to build 
under similar constraints.  There should have been an error earlier in the 
scramble output with more details on why building bx-python failed.  If you 
rerun scramble on just that egg, you should be able to recapture the output:

  % python ./scripts/scramble.py -e bx_python

--nate

>
>
>
> Regards,
> Shun
> ________________________________________
> From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
> [ja...@jamestaylor.org]
> Sent: 21 February 2013 16:07
> To: Shun Liang
> Cc: galaxy-u...@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Installing Galaxy on ARM Architecture
>
> You are definitely in uncharted territory with an arm server. Can you
> try building just bx-python itself and let us know what the errors
> are?
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
> On Thu, Feb 21, 2013 at 11:03 AM, Shun Liang <shun.li...@cruk.cam.ac.uk> 
> wrote:
>> Hi,
>>
>> I am trying to install Galaxy on an ARMV7 architecture Linux server. I ran
>> "run.sh" and failed because some of the python eggs could not be fetched. I
>> then have a look at "http://eggs.galaxyproject.org/"; and I have realized
>> there aren't any armv7 builds for those eggs.
>>
>> I then decided to build (or scramble) the eggs on my own. I ran
>> "scripts/scramble.py" and this also failed with the following message (after
>> building a lot of things):
>>
>> scramble(): Copied egg to:
>>  /nfs/users/galaxy_dist/eggs/twill-0.9-py2.7.egg
>> Traceback (most recent call last):
>>  File "scripts/scramble.py", line 26, in <module>
>>    eggs = c.scramble()
>>  File "/nfs/users/galaxy_dist/lib/galaxy/eggs/scramble.py", line 242, in
>> scramble
>>    raise last_exc # only 1 failure out of the crate, be more informative
>> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
>> failed for bx_python 0.7.1
>>
>>
>> May I ask what may cause this problem? Have I done anything wrong? Or, is it
>> even possible to install Galaxy on ARM architecture Linux?
>>
>>
>>
>> Many thanks,
>> Shun
>>
>>
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>  http://lists.bx.psu.edu/
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>  http://lists.bx.psu.edu/


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