Hi Shun,
Would you please share which third-party tools you are able to compile
on ARM? I'll be very interested in knowing about that. I'm thinking on
things like samtools, bowtie, tophat, cufflinks, bwa, ncbi_blast, etc.
Thanks,
Carlos
On Fri, Feb 22, 2013 at 10:51 AM, Shun Liang <Shun.Liang(a)cruk.cam.ac.uk> wrote:
Hi Nate,
After terminating the process which was listening 8080 I am now able to launch Galaxy.
Many thanks for you help,
Shun
________________________________________
From: Nate Coraor [nate(a)bx.psu.edu]
Sent: 22 February 2013 15:31
To: Shun Liang
Cc: James Taylor; galaxy-dev(a)lists.bx.psu.edu
Subject: Re: [galaxy-dev] Installing Galaxy on ARM Architecture
On Feb 22, 2013, at 10:21 AM, Shun Liang wrote:
> 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
This is a good sign.
> $ 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
This means that something is already listening on the port Galaxy is trying to use.
Assuming you did not change the port in universe_wsgi.ini, you can determine what process
it is with `lsof -i :8080`. Or you could change the port in universe_wsgi.ini to
something else.
--nate
> 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 [nate(a)bx.psu.edu]
> Sent: 21 February 2013 16:56
> To: Shun Liang
> Cc: James Taylor; galaxy-dev(a)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: james(a)taylorlab.org [james(a)taylorlab.org] on behalf of James Taylor
[james(a)jamestaylor.org]
>> Sent: 21 February 2013 16:07
>> To: Shun Liang
>> Cc: galaxy-user(a)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.Liang(a)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
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>>> use the Galaxy Development list:
>>>
>>>
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>>>
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>>> please use the interface at:
>>>
>>>
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>>
>> ___________________________________________________________
>> 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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