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.li...@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 [n...@bx.psu.edu] > Sent: 22 February 2013 15:31 > To: Shun Liang > Cc: James Taylor; galaxy-dev@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 [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/ >> >> > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
