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,
___
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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:
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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:
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To search Galaxy mailing lists use the unified search at:
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___
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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:
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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"
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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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[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/
