Invalid Galaxy URL: None - Installing Tools Shed
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/ aebrenne@uci.edu
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/ aebrenne@uci.edu ___________________________________________________________ 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/
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/ aebrenne@uci.edu ___________________________________________________________ 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/
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/ aebrenne@uci.edu On Wed, May 8, 2013 at 6:50 AM, Greg Von Kuster <greg@bx.psu.edu> 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/ aebrenne@uci.edu ___________________________________________________________ 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/
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 <dave@bx.psu.edu> 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/ aebrenne@uci.edu ___________________________________________________________ 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/
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 <p.j.a.cock@googlemail.com> 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 <dave@bx.psu.edu> 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/ aebrenne@uci.edu ___________________________________________________________ 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/
On Tue, Aug 6, 2013 at 6:11 PM, Greg Von Kuster <greg@bx.psu.edu> 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
On Aug 6, 2013, at 1:14 PM, Peter Cock <p.j.a.cock@googlemail.com> 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.
On Tue, Aug 6, 2013 at 6:22 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Aug 6, 2013, at 1:14 PM, Peter Cock <p.j.a.cock@googlemail.com> 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
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 <p.j.a.cock@googlemail.com> wrote:
On Tue, Aug 6, 2013 at 6:22 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Aug 6, 2013, at 1:14 PM, Peter Cock <p.j.a.cock@googlemail.com> 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
participants (4)
-
Adam Brenner -
Dave Bouvier -
Greg Von Kuster -
Peter Cock