Invalid Galaxy URL: None - Installing Tools Shed

classic Classic list List threaded Threaded
10 messages Options
Reply | Threaded
Open this post in threaded view
|

Invalid Galaxy URL: None - Installing Tools Shed

Adam Brenner
Howdy,

I am trying to install a tools shed item, Emboss, but when I do this
via the admin interface, I get the following text:

Repository installation is not possible due to an invalid Galaxy URL:
None. You may need to enable cookies in your browser.

I have searched the universe_wsgi.ini file and could not find anything
that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?

Thanks,
-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]
___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Dave Bouvier
Adam,

Normally, the Galaxy URL should be automatically determined and set in a
cookie during the repository installation process.

To help track down this issue, could you provide the revision of Galaxy
you're running, and the end of the paster.log file when this error occurs?


    --Dave B.

On 5/7/13 20:13:38.000, Adam Brenner wrote:

> Howdy,
>
> I am trying to install a tools shed item, Emboss, but when I do this
> via the admin interface, I get the following text:
>
> Repository installation is not possible due to an invalid Galaxy URL:
> None. You may need to enable cookies in your browser.
>
> I have searched the universe_wsgi.ini file and could not find anything
> that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?
>
> Thanks,
> -Adam
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> Research Computing Support
> Office of Information Technology
> http://www.oit.uci.edu/rcs/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> [hidden email]
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Greg Von Kuster
In addition, it's helpful to know which browser you are using. Safari has fairly strict policies on 3rd-party cookies if you have them blocked.  Chrome and firefox are less strict, so unblocking 3rd-party cookies if using Safari or simply switching to chrome or firefox will probably solve this issue.

Greg Von Kuster

On May 8, 2013, at 9:45 AM, Dave Bouvier wrote:

> Adam,
>
> Normally, the Galaxy URL should be automatically determined and set in a cookie during the repository installation process.
>
> To help track down this issue, could you provide the revision of Galaxy you're running, and the end of the paster.log file when this error occurs?
>
>
>  --Dave B.
>
> On 5/7/13 20:13:38.000, Adam Brenner wrote:
>> Howdy,
>>
>> I am trying to install a tools shed item, Emboss, but when I do this
>> via the admin interface, I get the following text:
>>
>> Repository installation is not possible due to an invalid Galaxy URL:
>> None. You may need to enable cookies in your browser.
>>
>> I have searched the universe_wsgi.ini file and could not find anything
>> that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?
>>
>> Thanks,
>> -Adam
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> Research Computing Support
>> Office of Information Technology
>> http://www.oit.uci.edu/rcs/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> [hidden email]
>> ___________________________________________________________
>> 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:
>>  http://lists.bx.psu.edu/
>>
>> 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:
> http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Adam Brenner
Greg,

Thanks for the tip on Safari. I have switched to another browser and
working now!

Thanks,
-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]


On Wed, May 8, 2013 at 6:50 AM, Greg Von Kuster <[hidden email]> wrote:

> In addition, it's helpful to know which browser you are using. Safari has fairly strict policies on 3rd-party cookies if you have them blocked.  Chrome and firefox are less strict, so unblocking 3rd-party cookies if using Safari or simply switching to chrome or firefox will probably solve this issue.
>
> Greg Von Kuster
>
> On May 8, 2013, at 9:45 AM, Dave Bouvier wrote:
>
>> Adam,
>>
>> Normally, the Galaxy URL should be automatically determined and set in a cookie during the repository installation process.
>>
>> To help track down this issue, could you provide the revision of Galaxy you're running, and the end of the paster.log file when this error occurs?
>>
>>
>>  --Dave B.
>>
>> On 5/7/13 20:13:38.000, Adam Brenner wrote:
>>> Howdy,
>>>
>>> I am trying to install a tools shed item, Emboss, but when I do this
>>> via the admin interface, I get the following text:
>>>
>>> Repository installation is not possible due to an invalid Galaxy URL:
>>> None. You may need to enable cookies in your browser.
>>>
>>> I have searched the universe_wsgi.ini file and could not find anything
>>> that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?
>>>
>>> Thanks,
>>> -Adam
>>>
>>> --
>>> Adam Brenner
>>> Computer Science, Undergraduate Student
>>> Donald Bren School of Information and Computer Sciences
>>>
>>> Research Computing Support
>>> Office of Information Technology
>>> http://www.oit.uci.edu/rcs/
>>>
>>> University of California, Irvine
>>> www.ics.uci.edu/~aebrenne/
>>> [hidden email]
>>> ___________________________________________________________
>>> 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:
>>>  http://lists.bx.psu.edu/
>>>
>>> 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:
>> http://lists.bx.psu.edu/
>>
>> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Peter Cock
In reply to this post by Dave Bouvier
Hi all,

I'm (finally) attempting to install a tool from the main Tool Shed into
a local Galaxy instance, using Firefox, and got the same red error
that Adam reported (below):

"Repository installation is not possible due to an invalid Galaxy URL:
None. You may need to enable cookies in your browser."

Might my apache rewrite be causing this? My galaxy server is
available on the normal http port 80 as servername/galaxy and
in universe_wsgi.ini I have set:

cookie_path = /galaxy

Is there another setting which I need to fill in (perhaps something
missing in older copies of universe_wsgi.ini.sample)?

Thanks,

Peter

On Wed, May 8, 2013 at 2:45 PM, Dave Bouvier <[hidden email]> wrote:

> Adam,
>
> Normally, the Galaxy URL should be automatically determined and set in a
> cookie during the repository installation process.
>
> To help track down this issue, could you provide the revision of Galaxy
> you're running, and the end of the paster.log file when this error occurs?
>
>
>    --Dave B.
>
>
> On 5/7/13 20:13:38.000, Adam Brenner wrote:
>>
>> Howdy,
>>
>> I am trying to install a tools shed item, Emboss, but when I do this
>> via the admin interface, I get the following text:
>>
>> Repository installation is not possible due to an invalid Galaxy URL:
>> None. You may need to enable cookies in your browser.
>>
>> I have searched the universe_wsgi.ini file and could not find anything
>> that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?
>>
>> Thanks,
>> -Adam
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> Research Computing Support
>> Office of Information Technology
>> http://www.oit.uci.edu/rcs/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> [hidden email]
>> ___________________________________________________________
>> 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:
>>    http://lists.bx.psu.edu/
>>
>> 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:
>  http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Greg Von Kuster
Hi peter,

Do you have cookies blocked in your Firefox browser?  Does your cookie_path setting work for what you've configured in your apache prefix?  It's impossible to tell what specifically could be causing this in your environment, but it's definitely related to cookies.

Greg Von Kuster


On Aug 6, 2013, at 12:57 PM, Peter Cock <[hidden email]> wrote:

> Hi all,
>
> I'm (finally) attempting to install a tool from the main Tool Shed into
> a local Galaxy instance, using Firefox, and got the same red error
> that Adam reported (below):
>
> "Repository installation is not possible due to an invalid Galaxy URL:
> None. You may need to enable cookies in your browser."
>
> Might my apache rewrite be causing this? My galaxy server is
> available on the normal http port 80 as servername/galaxy and
> in universe_wsgi.ini I have set:
>
> cookie_path = /galaxy
>
> Is there another setting which I need to fill in (perhaps something
> missing in older copies of universe_wsgi.ini.sample)?
>
> Thanks,
>
> Peter
>
> On Wed, May 8, 2013 at 2:45 PM, Dave Bouvier <[hidden email]> wrote:
>> Adam,
>>
>> Normally, the Galaxy URL should be automatically determined and set in a
>> cookie during the repository installation process.
>>
>> To help track down this issue, could you provide the revision of Galaxy
>> you're running, and the end of the paster.log file when this error occurs?
>>
>>
>>   --Dave B.
>>
>>
>> On 5/7/13 20:13:38.000, Adam Brenner wrote:
>>>
>>> Howdy,
>>>
>>> I am trying to install a tools shed item, Emboss, but when I do this
>>> via the admin interface, I get the following text:
>>>
>>> Repository installation is not possible due to an invalid Galaxy URL:
>>> None. You may need to enable cookies in your browser.
>>>
>>> I have searched the universe_wsgi.ini file and could not find anything
>>> that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?
>>>
>>> Thanks,
>>> -Adam
>>>
>>> --
>>> Adam Brenner
>>> Computer Science, Undergraduate Student
>>> Donald Bren School of Information and Computer Sciences
>>>
>>> Research Computing Support
>>> Office of Information Technology
>>> http://www.oit.uci.edu/rcs/
>>>
>>> University of California, Irvine
>>> www.ics.uci.edu/~aebrenne/
>>> [hidden email]
>>> ___________________________________________________________
>>> 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:
>>>   http://lists.bx.psu.edu/
>>>
>>> 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:
>> http://lists.bx.psu.edu/
>>
>> 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:
>  http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Peter Cock
On Tue, Aug 6, 2013 at 6:11 PM, Greg Von Kuster <[hidden email]> wrote:
> Hi peter,
>
> Do you have cookies blocked in your Firefox browser?  Does your
> cookie_path setting work for what you've configured in your apache
> prefix?

Yes, logging into my Galaxy and using it works fine - I can close
tabs and go back and still be logged in.

> It's impossible to tell what specifically could be causing this
> in your environment, but it's definitely related to cookies.
>
> Greg Von Kuster

My Firefox is setup to accept cookies until the expire, but not
to accept third-party cookies.

Do I need to worry about cross-site cookies for my Galaxy server
talking to the Main (or Test) Tool Shed?

Peter
___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Greg Von Kuster

On Aug 6, 2013, at 1:14 PM, Peter Cock <[hidden email]> wrote:

> My Firefox is setup to accept cookies until the expire, but not
> to accept third-party cookies.
>
> Do I need to worry about cross-site cookies for my Galaxy server
> talking to the Main (or Test) Tool Shed?
>

Yes, this must be the problem - third-party cookies are used to store information between the Galaxy and Tool Shed applications.


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Peter Cock
On Tue, Aug 6, 2013 at 6:22 PM, Greg Von Kuster <[hidden email]> wrote:

>
> On Aug 6, 2013, at 1:14 PM, Peter Cock <[hidden email]> wrote:
>
>> My Firefox is setup to accept cookies until the expire, but not
>> to accept third-party cookies.
>>
>> Do I need to worry about cross-site cookies for my Galaxy server
>> talking to the Main (or Test) Tool Shed?
>>
>
> Yes, this must be the problem - third-party cookies are used to store
> information between the Galaxy and Tool Shed applications.
>

Confirmed, I relaxed the 3rd party cookie setting to "from visited",
now I get a new error message which is much easier to understand
(and which I will look at tomorrow):

<quote>
The tool_config_file setting in universe_wsgi.ini must include at
least one shed tool configuration file name with a <toolbox> tag that
includes a tool_path attribute value which is a directory relative to
the Galaxy installation directory in order to automatically install
tools from a Galaxy tool shed (e.g., the file name shed_tool_conf.xml
whose <toolbox> tag is <toolbox tool_path="../shed_tools">).

See the Installation of Galaxy tool shed repository tools into a local
Galaxy instance section of the Galaxy tool shed wiki for all of the
details.
</quote>

Getting back to the cookie problem, perhaps the error message
could use the phrase "third-party cookies" rather than just
plain "cookies"?

Thanks,

Peter
___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Invalid Galaxy URL: None - Installing Tools Shed

Greg Von Kuster
You just need something like the following in your universe_wsgi.ini.

# Tool config files, defines what tools are available in Galaxy.
# Tools can be locally developed or installed from Galaxy tool sheds.
tool_config_file = tool_conf.xml,shed_tool_conf.xml



On Aug 6, 2013, at 1:27 PM, Peter Cock <[hidden email]> wrote:

On Tue, Aug 6, 2013 at 6:22 PM, Greg Von Kuster <[hidden email]> wrote:

On Aug 6, 2013, at 1:14 PM, Peter Cock <[hidden email]> wrote:

My Firefox is setup to accept cookies until the expire, but not
to accept third-party cookies.

Do I need to worry about cross-site cookies for my Galaxy server
talking to the Main (or Test) Tool Shed?


Yes, this must be the problem - third-party cookies are used to store
information between the Galaxy and Tool Shed applications.


Confirmed, I relaxed the 3rd party cookie setting to "from visited",
now I get a new error message which is much easier to understand
(and which I will look at tomorrow):

<quote>
The tool_config_file setting in universe_wsgi.ini must include at
least one shed tool configuration file name with a <toolbox> tag that
includes a tool_path attribute value which is a directory relative to
the Galaxy installation directory in order to automatically install
tools from a Galaxy tool shed (e.g., the file name shed_tool_conf.xml
whose <toolbox> tag is <toolbox tool_path="../shed_tools">).

See the Installation of Galaxy tool shed repository tools into a local
Galaxy instance section of the Galaxy tool shed wiki for all of the
details.
</quote>

Getting back to the cookie problem, perhaps the error message
could use the phrase "third-party cookies" rather than just
plain "cookies"?

Thanks,

Peter


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/