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 <p.j.a.c...@googlemail.com> 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 <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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