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@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: 21 February 2013 16:07 To: Shun Liang Cc: galaxy-user@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@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:
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:
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 [nate@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: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: 21 February 2013 16:07 To: Shun Liang Cc: galaxy-user@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@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:
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:
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@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: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: 21 February 2013 16:07 To: Shun Liang Cc: galaxy-user@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@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:
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:
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@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 [nate@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: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: 21 February 2013 16:07 To: Shun Liang Cc: galaxy-user@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@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:
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:
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@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@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 [nate@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: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: 21 February 2013 16:07 To: Shun Liang Cc: galaxy-user@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@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:
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:
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:
galaxy-dev@lists.galaxyproject.org
-
Carlos Borroto -
Nate Coraor -
Shun Liang