Re: [galaxy-dev] Error installing cummeRbund tool
Hi Peter,
Ah! I was looking for where to report bugs; thanks for leading me in
the right direction!
Seems the problem I've encountered has been previously reported:
https://github.com/galaxyproject/tools-devteam/issues/317 . I'll keep
an eye on this bug report and see if I can somehow contribute.
Thanks a lot for your help!
Ray
On Tue, Jun 7, 2016 at 3:05 AM, Peter Cock wrote:
> Hi Ray,
>
> Each tool should have a contact the author option and a home
> page listed on the Tool Shed. Sometimes the README file
> says explicitly where they would like bugs reported.
>
> In this case, the devteam Tool Shed packages are here:
> https://github.com/galaxyproject/tools-devteam
>
> You can report issues for those tools/pacakges at
> https://github.com/galaxyproject/tools-devteam/issues
>
> (Because this these are managed by the Galaxy developers
> themselves, then reporting it on this mailing list should also
> reach the relevant people.)
>
> Peter
>
>
> On Tue, Jun 7, 2016 at 4:40 AM, Raymond Wan wrote:
>> Dear all,
>>
>> Sorry to bring this up again, but I've been so far unable to solve
>> this problem. After trying to install various combination of things
>> and looking further away from the Exception messages, I guess I have
>> located the cause of the problem. It seems at least two dependencies
>> no longer exist on the server in a particular location. These are two
>> more lines in the paster log file:
>>
>> tool_shed.galaxy_install.install_manager ERROR 2016-06-03 14:47:14,508
>> Error installing tool dependency libpng version 1.6.7: Unable to
>> locate required tool shed repository named package_libpng_1_6_7 owned
>> by devteam with revision 3de32cd300a9.
>> tool_shed.galaxy_install.install_manager ERROR 2016-06-03 14:47:15,536
>> Error installing tool dependency freetype version 2.5.2: Unable to
>> locate required tool shed repository named package_freetype_2_5_2
>> owned by devteam with revision a65217367e4a.
>>
>> So both of these are dependencies of cummeRbund. Is there a
>> work-around for this kind of problem? For example, if I installed
>> libpng and/or freetype using CentOS' package manager (i.e., rpm), will
>> it no longer search for this dependency? Alternatively, is there
>> someone I should notify about this kind of problem in the Tool Shed?
>>
>> Thank you for your help!
>>
>> Ray
>>
>>
>>
>>
>>
>> On Fri, Jun 3, 2016 at 1:08 AM, Raymond Wan wrote:
>>> Dear all,
>>>
>>> I'm trying to install a Galaxy tool (cummeRbund; the one from devteam)
>>> and I'm getting the following error during installation:
>>>
>>> -
>>> Proxy Error
>>>
>>> The proxy server received an invalid response from an upstream server.
>>> The proxy server could not handle the request POST
>>> /admin_toolshed/prepare_for_install.
>>>
>>> Reason: Error reading from remote server
>>> -
>>>
>>> In paster.log, I see this:
>>>
>>>
>>> Exception happened during processing of request from ('127.0.0.1', 35420)
>>> Traceback (most recent call last):
>>> File "/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
>>> line 1068, in process_request_in_thread
>>> self.finish_request(request, client_address)
>>> File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request
>>> self.RequestHandlerClass(request, client_address, self)
>>> File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__
>>> self.finish()
>>> File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish
>>> self.wfile.flush()
>>> File "/usr/lib64/python2.6/socket.py", line 303, in flush
>>> self._sock.sendall(buffer(data, write_offset, buffer_size))
>>> error: [Errno 32] Broken pipe
>>>
>>>
>>> Does this mean there's a problem on our side, or perhaps there is a
>>> file missing from the tool (or the connection to the Toolshed has a
>>> problem)?
>>>
>>> Any suggestions as to what I should look for? I first tried 2 days
>>> ago and waited until now to try again -- still the same problem.
>>>
>>> Thank you!
>>>
>>> Ray
>> ___
>> 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:
>> https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Error installing cummeRbund tool
Hi Ray,
Each tool should have a contact the author option and a home
page listed on the Tool Shed. Sometimes the README file
says explicitly where they would like bugs reported.
In this case, the devteam Tool Shed packages are here:
https://github.com/galaxyproject/tools-devteam
You can report issues for those tools/pacakges at
https://github.com/galaxyproject/tools-devteam/issues
(Because this these are managed by the Galaxy developers
themselves, then reporting it on this mailing list should also
reach the relevant people.)
Peter
On Tue, Jun 7, 2016 at 4:40 AM, Raymond Wan wrote:
> Dear all,
>
> Sorry to bring this up again, but I've been so far unable to solve
> this problem. After trying to install various combination of things
> and looking further away from the Exception messages, I guess I have
> located the cause of the problem. It seems at least two dependencies
> no longer exist on the server in a particular location. These are two
> more lines in the paster log file:
>
> tool_shed.galaxy_install.install_manager ERROR 2016-06-03 14:47:14,508
> Error installing tool dependency libpng version 1.6.7: Unable to
> locate required tool shed repository named package_libpng_1_6_7 owned
> by devteam with revision 3de32cd300a9.
> tool_shed.galaxy_install.install_manager ERROR 2016-06-03 14:47:15,536
> Error installing tool dependency freetype version 2.5.2: Unable to
> locate required tool shed repository named package_freetype_2_5_2
> owned by devteam with revision a65217367e4a.
>
> So both of these are dependencies of cummeRbund. Is there a
> work-around for this kind of problem? For example, if I installed
> libpng and/or freetype using CentOS' package manager (i.e., rpm), will
> it no longer search for this dependency? Alternatively, is there
> someone I should notify about this kind of problem in the Tool Shed?
>
> Thank you for your help!
>
> Ray
>
>
>
>
>
> On Fri, Jun 3, 2016 at 1:08 AM, Raymond Wan wrote:
>> Dear all,
>>
>> I'm trying to install a Galaxy tool (cummeRbund; the one from devteam)
>> and I'm getting the following error during installation:
>>
>> -
>> Proxy Error
>>
>> The proxy server received an invalid response from an upstream server.
>> The proxy server could not handle the request POST
>> /admin_toolshed/prepare_for_install.
>>
>> Reason: Error reading from remote server
>> -
>>
>> In paster.log, I see this:
>>
>>
>> Exception happened during processing of request from ('127.0.0.1', 35420)
>> Traceback (most recent call last):
>> File "/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
>> line 1068, in process_request_in_thread
>> self.finish_request(request, client_address)
>> File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request
>> self.RequestHandlerClass(request, client_address, self)
>> File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__
>> self.finish()
>> File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish
>> self.wfile.flush()
>> File "/usr/lib64/python2.6/socket.py", line 303, in flush
>> self._sock.sendall(buffer(data, write_offset, buffer_size))
>> error: [Errno 32] Broken pipe
>>
>>
>> Does this mean there's a problem on our side, or perhaps there is a
>> file missing from the tool (or the connection to the Toolshed has a
>> problem)?
>>
>> Any suggestions as to what I should look for? I first tried 2 days
>> ago and waited until now to try again -- still the same problem.
>>
>> Thank you!
>>
>> Ray
> ___
> 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:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error installing cummeRbund tool
Dear all,
Sorry to bring this up again, but I've been so far unable to solve
this problem. After trying to install various combination of things
and looking further away from the Exception messages, I guess I have
located the cause of the problem. It seems at least two dependencies
no longer exist on the server in a particular location. These are two
more lines in the paster log file:
tool_shed.galaxy_install.install_manager ERROR 2016-06-03 14:47:14,508
Error installing tool dependency libpng version 1.6.7: Unable to
locate required tool shed repository named package_libpng_1_6_7 owned
by devteam with revision 3de32cd300a9.
tool_shed.galaxy_install.install_manager ERROR 2016-06-03 14:47:15,536
Error installing tool dependency freetype version 2.5.2: Unable to
locate required tool shed repository named package_freetype_2_5_2
owned by devteam with revision a65217367e4a.
So both of these are dependencies of cummeRbund. Is there a
work-around for this kind of problem? For example, if I installed
libpng and/or freetype using CentOS' package manager (i.e., rpm), will
it no longer search for this dependency? Alternatively, is there
someone I should notify about this kind of problem in the Tool Shed?
Thank you for your help!
Ray
On Fri, Jun 3, 2016 at 1:08 AM, Raymond Wan wrote:
> Dear all,
>
> I'm trying to install a Galaxy tool (cummeRbund; the one from devteam)
> and I'm getting the following error during installation:
>
> -
> Proxy Error
>
> The proxy server received an invalid response from an upstream server.
> The proxy server could not handle the request POST
> /admin_toolshed/prepare_for_install.
>
> Reason: Error reading from remote server
> -
>
> In paster.log, I see this:
>
>
> Exception happened during processing of request from ('127.0.0.1', 35420)
> Traceback (most recent call last):
> File "/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
> self.finish_request(request, client_address)
> File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request
> self.RequestHandlerClass(request, client_address, self)
> File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__
> self.finish()
> File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish
> self.wfile.flush()
> File "/usr/lib64/python2.6/socket.py", line 303, in flush
> self._sock.sendall(buffer(data, write_offset, buffer_size))
> error: [Errno 32] Broken pipe
>
>
> Does this mean there's a problem on our side, or perhaps there is a
> file missing from the tool (or the connection to the Toolshed has a
> problem)?
>
> Any suggestions as to what I should look for? I first tried 2 days
> ago and waited until now to try again -- still the same problem.
>
> Thank you!
>
> Ray
___
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
