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 <rwan.w...@gmail.com> 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 <rwan.w...@gmail.com> 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
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