[galaxy-dev] Where is the output of tools stored in Galaxy?

[Sachit Adhikari]

Hello Everyone,

*Merry Christmas and Happy New Year*
*
*
I was wondering where are the output of the tools stored in the machine
where the galaxy is hosted? And, can I change the path of the output of the
tools?

Thanks,

Sachit
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[galaxy-dev] Tool reinstall breaking again...

[Franco Caramia]

Hi list,

Merry Christmas to all!

I installed the "homer" tool from the main galaxy toolshed and then made a
pull to revision : 8414:36ad8aa7b922

Then uninstalled the tool and tried to reinstall and got the following
error:


URL:
http://115.146.94.148/admin_toolshed/reselect_tool_panel_section?id=b9a95d0facd286e3
Module paste.exceptions.errormiddleware:*144* in __call__
>>

app_iter *=* self*.*application*(*environ*,* sr_checker*)*
Module paste.debug.prints:*106* in __call__
>>

environ*,* self*.*app*)*
Module paste.wsgilib:*543* in intercept_output
>>

app_iter *=* application*(*environ*,* replacement_start_response*)*
Module paste.recursive:*84* in __call__
>>

*return* self*.*application*(*environ*,* start_response*)*
Module paste.httpexceptions:*633* in __call__
>>

*return* self*.*application*(*environ*,* start_response*)*
Module galaxy.web.framework.base:*160* in __call__
>>

body *=* method*(* trans*,* kwargs *)*
Module galaxy.web.framework:*206* in decorator
>>

*return* func*(* self*,* trans*,* ***args*,* kwargs *)*
Module galaxy.webapps.galaxy.controllers.admin_toolshed:*1445* in
reselect_tool_panel_section
>>

response *=* urllib2*.*urlopen*(* url *)*
Module urllib2:*126* in urlopen
>>

*return* _opener*.*open*(*url*,* data*,* timeout*)*
Module urllib2:*406* in open
>>

response *=* meth*(*req*,* response*)*
Module urllib2:*519* in http_response
>>

'http'*,* request*,* response*,* code*,* msg*,* hdrs*)*
Module urllib2:*444* in error
>>

*return* self*.*_call_chain*(args*)*
Module urllib2:*378* in _call_chain
>>

result *=* func*(args*)*
Module urllib2:*527* in http_error_default
>>

*raise* HTTPError*(*req*.*get_full_url*(**)**,* code*,* msg*,* hdrs*,* fp*)*
*HTTPError: HTTP Error 404: Not Found*


Any ideas on what could be happening??
I did the same before the pull and everything seemed to be working
correctly...

Thanks,

Franco
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Re: [galaxy-dev] How to refresh the tool panel in Galaxy?

[Huayan Gao]

Thank you Alex and Ross. This is a totally new tool so there is not record
yet. So I guess it will not work without restarting the server.

Best,
Huayan


On Sat, Dec 15, 2012 at 1:36 AM, Oleksandr Moskalenko wrote:

> There's also a shortcut that avoids having to click through the menus
> every time. You can use a reload URL. For instance, if you were working
> with a local instance and developing the tool 'mytool'. You can open the
> following url, keep that page open and reload it when necessary to update
> the modified wrapper in the galaxy.
>
>
> http://localhost:8080/admin/reload_tool?reload_tool_button=Reload&tool_id=mytool
>
> Regards,
>
> Alex
>
> On Dec 12, 2012, at 9:21 PM, Ross  wrote:
>
> After making changes to the tool xml, you can refresh any tool using the
> admin menu
> Reload a tool's configuration
> option.
> This only works for tools loaded at startup and AFAIK there is currently
> no way to load a brand new tool after Galaxy has started other than via the
> toolshed installation option or a server restart.
> If you edit a wrapper (eg perl or python) script that is called by a tool
> xml, it loads afresh for every subsequent job - no need to do anything to
> the server.
>
> On Thu, Dec 13, 2012 at 12:10 PM, Huayan Gao  wrote:
>
>> Dear all,
>>
>> I just want to follow up with this question(see email below). I am afraid
>> that it is lost in the traffic.
>>
>> Thanks,
>> Huayan
>>
>>
>> On Fri, Dec 7, 2012 at 12:48 PM, Huayan Gao  wrote:
>>
>>> Hi,
>>>
>>> I am trying to add a tool into Galaxy. So far everything is ok except
>>> that I need to restart the server to make the tool showing up in the tool
>>> panel.
>>>
>>> So my question is that how to refresh the tool panel without restarting
>>> the server?
>>>
>>> After I install a tool from toolshed, I can see the tool immediately
>>> from the tool panel. This is exactly the function I want to implement in
>>> python. I was reading the code but too complicated. Could you point me the
>>> right place(code)?
>>>
>>> Thanks a lot.
>>>
>>> Best,
>>> Huayan
>>>
>>
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