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.work@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.work@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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