Re: [galaxy-dev] local toolshed not working
And thank you for making us aware of this issue, we've updated the sample configs to include that option and its default value. - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 04/28/2016 11:02 AM, Vincent Cahais wrote: It's working, Thanks Dave. Le 28/04/2016 16:40, Dave Bouvier a écrit : Vincent, Thanks, that looks like either a different bug, or the fix hasn't made it to the master branch yet. One possible workaround you could try, while I confirm which is the case, is to set the following option in your tool_shed.ini somewhere after [app:main] use_printdebug = False - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 04/28/2016 09:54 AM, Vincent Cahais wrote: >git show commit b79474083b08860923f7f28fc1e7442b53f925db Merge: 7c94ac8 5aefe1b Author: Martin Cech Date: Wed Apr 20 15:22:20 2016 -0400 Merge pull request #2206 from dannon/master Sanity check of master update. Le 28/04/2016 15:40, Dave Bouvier a écrit : Vincent, Could you provide the output of `git show` in your Galaxy root? This error message looks like a bug that was fixed in 0d616af28a175bae8e193f429a18f97cd8b274ec. - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 04/28/2016 09:26 AM, Vincent Cahais wrote: Hi everyone, I'm trying to set up a new local toolshed with a fresh install of galaxy. I can run the server, create repositories and upload files. But when I try to install a tool in galaxy it fail with a server error. In the tool_shed_webapp.log I have the following error : Exception happened during processing of request from ('**.**.**.**', 41026) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 652, in __init__ self.handle() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 459, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 454, in handle_one_request self.wsgi_execute() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 304, in wsgi_execute self.wsgi_start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/urlmap.py", line 216, in __call__ return app(environ, start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/debug/prints.py", line 107, in __call__ environ, self.app) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/wsgilib.py", line 547, in intercept_output if data[0] is None: IndexError: list index out of range Removing PID file tool_shed_webapp.pid Cheers, ___ 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] local toolshed not working
It's working, Thanks Dave. Le 28/04/2016 16:40, Dave Bouvier a écrit : > Vincent, > > Thanks, that looks like either a different bug, or the fix hasn't made > it to the master branch yet. One possible workaround you could try, > while I confirm which is the case, is to set the following option in > your tool_shed.ini somewhere after [app:main] > > use_printdebug = False > > - > Dave Bouvier > http://galaxyproject.org > http://usegalaxy.org > > On 04/28/2016 09:54 AM, Vincent Cahais wrote: >> >git show >> >> commit b79474083b08860923f7f28fc1e7442b53f925db >> Merge: 7c94ac8 5aefe1b >> Author: Martin Cech >> Date: Wed Apr 20 15:22:20 2016 -0400 >> >> Merge pull request #2206 from dannon/master >> >> Sanity check of master update. >> >> >> >> Le 28/04/2016 15:40, Dave Bouvier a écrit : >>> Vincent, >>> >>> Could you provide the output of `git show` in your Galaxy root? This >>> error message looks like a bug that was fixed in >>> 0d616af28a175bae8e193f429a18f97cd8b274ec. >>> >>> - >>> Dave Bouvier >>> http://galaxyproject.org >>> http://usegalaxy.org >>> >>> On 04/28/2016 09:26 AM, Vincent Cahais wrote: Hi everyone, I'm trying to set up a new local toolshed with a fresh install of galaxy. I can run the server, create repositories and upload files. But when I try to install a tool in galaxy it fail with a server error. In the tool_shed_webapp.log I have the following error : Exception happened during processing of request from ('**.**.**.**', 41026) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 652, in __init__ self.handle() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 459, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 454, in handle_one_request self.wsgi_execute() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 304, in wsgi_execute self.wsgi_start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/urlmap.py", line 216, in __call__ return app(environ, start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/debug/prints.py", line 107, in __call__ environ, self.app) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/wsgilib.py", line 547, in intercept_output if data[0] is None: IndexError: list index out of range Removing PID file tool_shed_webapp.pid Cheers, ___ 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] local toolshed not working
Vincent, Thanks, that looks like either a different bug, or the fix hasn't made it to the master branch yet. One possible workaround you could try, while I confirm which is the case, is to set the following option in your tool_shed.ini somewhere after [app:main] use_printdebug = False - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 04/28/2016 09:54 AM, Vincent Cahais wrote: >git show commit b79474083b08860923f7f28fc1e7442b53f925db Merge: 7c94ac8 5aefe1b Author: Martin Cech Date: Wed Apr 20 15:22:20 2016 -0400 Merge pull request #2206 from dannon/master Sanity check of master update. Le 28/04/2016 15:40, Dave Bouvier a écrit : Vincent, Could you provide the output of `git show` in your Galaxy root? This error message looks like a bug that was fixed in 0d616af28a175bae8e193f429a18f97cd8b274ec. - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 04/28/2016 09:26 AM, Vincent Cahais wrote: Hi everyone, I'm trying to set up a new local toolshed with a fresh install of galaxy. I can run the server, create repositories and upload files. But when I try to install a tool in galaxy it fail with a server error. In the tool_shed_webapp.log I have the following error : Exception happened during processing of request from ('**.**.**.**', 41026) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 652, in __init__ self.handle() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 459, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 454, in handle_one_request self.wsgi_execute() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 304, in wsgi_execute self.wsgi_start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/urlmap.py", line 216, in __call__ return app(environ, start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/debug/prints.py", line 107, in __call__ environ, self.app) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/wsgilib.py", line 547, in intercept_output if data[0] is None: IndexError: list index out of range Removing PID file tool_shed_webapp.pid Cheers, ___ 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] local toolshed not working
>git show commit b79474083b08860923f7f28fc1e7442b53f925db Merge: 7c94ac8 5aefe1b Author: Martin Cech Date: Wed Apr 20 15:22:20 2016 -0400 Merge pull request #2206 from dannon/master Sanity check of master update. Le 28/04/2016 15:40, Dave Bouvier a écrit : > Vincent, > > Could you provide the output of `git show` in your Galaxy root? This > error message looks like a bug that was fixed in > 0d616af28a175bae8e193f429a18f97cd8b274ec. > > - > Dave Bouvier > http://galaxyproject.org > http://usegalaxy.org > > On 04/28/2016 09:26 AM, Vincent Cahais wrote: >> Hi everyone, >> >> I'm trying to set up a new local toolshed with a fresh install of >> galaxy. >> I can run the server, create repositories and upload files. But when I >> try to install a tool in galaxy it fail with a server error. >> >> In the tool_shed_webapp.log I have the following error : >> >> >> Exception happened during processing of request from ('**.**.**.**', >> 41026) >> Traceback (most recent call last): >> File >> "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", >> >> >> line 1085, in process_request_in_thread >> self.finish_request(request, client_address) >> File "/usr/lib/python2.7/SocketServer.py", line 331, in >> finish_request >> self.RequestHandlerClass(request, client_address, self) >> File "/usr/lib/python2.7/SocketServer.py", line 652, in __init__ >> self.handle() >> File >> "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", >> >> >> line 459, in handle >> BaseHTTPRequestHandler.handle(self) >> File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle >> self.handle_one_request() >> File >> "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", >> >> >> line 454, in handle_one_request >> self.wsgi_execute() >> File >> "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", >> >> >> line 304, in wsgi_execute >> self.wsgi_start_response) >> File >> "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/urlmap.py", >> >> >> line 216, in __call__ >> return app(environ, start_response) >> File >> "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/debug/prints.py", >> >> >> line 107, in __call__ >> environ, self.app) >> File >> "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/wsgilib.py", >> >> >> line 547, in intercept_output >> if data[0] is None: >> IndexError: list index out of range >> >> Removing PID file tool_shed_webapp.pid >> >> >> Cheers, >> ___ >> 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] local toolshed not working
Vincent, Could you provide the output of `git show` in your Galaxy root? This error message looks like a bug that was fixed in 0d616af28a175bae8e193f429a18f97cd8b274ec. - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 04/28/2016 09:26 AM, Vincent Cahais wrote: Hi everyone, I'm trying to set up a new local toolshed with a fresh install of galaxy. I can run the server, create repositories and upload files. But when I try to install a tool in galaxy it fail with a server error. In the tool_shed_webapp.log I have the following error : Exception happened during processing of request from ('**.**.**.**', 41026) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 652, in __init__ self.handle() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 459, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 454, in handle_one_request self.wsgi_execute() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 304, in wsgi_execute self.wsgi_start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/urlmap.py", line 216, in __call__ return app(environ, start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/debug/prints.py", line 107, in __call__ environ, self.app) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/wsgilib.py", line 547, in intercept_output if data[0] is None: IndexError: list index out of range Removing PID file tool_shed_webapp.pid Cheers, ___ 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/
[galaxy-dev] local toolshed not working
Hi everyone, I'm trying to set up a new local toolshed with a fresh install of galaxy. I can run the server, create repositories and upload files. But when I try to install a tool in galaxy it fail with a server error. In the tool_shed_webapp.log I have the following error : Exception happened during processing of request from ('**.**.**.**', 41026) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 652, in __init__ self.handle() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 459, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 454, in handle_one_request self.wsgi_execute() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 304, in wsgi_execute self.wsgi_start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/urlmap.py", line 216, in __call__ return app(environ, start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/debug/prints.py", line 107, in __call__ environ, self.app) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/wsgilib.py", line 547, in intercept_output if data[0] is None: IndexError: list index out of range Removing PID file tool_shed_webapp.pid Cheers, ___ 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/