Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy
Sergei Ryazansky wrote:
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the "redirected to non-http(s): /root" error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance!
Hi Sergei, If your Galaxy server is behind a proxy server serving via https, have you set the following header: RequestHeader set X-URL-SCHEME https Please see the "SSL" section of the ApacheProxy page for more information: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy --nate
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Hi Nate, No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the mentioned above error. 06.07.2011 22:30, Nate Coraor пишет:
Sergei Ryazansky wrote:
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the "redirected to non-http(s): /root" error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance! Hi Sergei,
If your Galaxy server is behind a proxy server serving via https, have you set the following header:
RequestHeader set X-URL-SCHEME https
Please see the "SSL" section of the ApacheProxy page for more information:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
--nat
Hi all, I would like to update the issue. I have found the following thread from the galaxy-dev list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html and according to the suggestion from it I have modified the UCSC_SITES in lib/galaxy/web/framework/__init__.py and 'sites' in lib/galaxy/security/__init__.py. Now these files contatin the url of our local mirror. After these changing the calling of display of bed file in local UCSC Genome Browser results in the following error message: "Unrecognized format line 1 of http://dmbcserv.dyndns.org/galaxy/root/display_as?id=436&display_app=ucsc&authz_method=display_at: You are not allowed to access this dataset. (note: chrom names are case sensitive)" You can check this on our public Galaxy mirror: http://dmbcserv.dyndns.org/galaxy. Have you any idea how to fix this? 2011/7/7 Sergei Ryazansky <s.ryazansky@gmail.com>
Hi Nate,
No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the mentioned above error.
06.07.2011 22:30, Nate Coraor пишет:
Sergei Ryazansky wrote:
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the "redirected to non-http(s): /root" error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance!
Hi Sergei,
If your Galaxy server is behind a proxy server serving via https, have you set the following header:
RequestHeader set X-URL-SCHEME https
Please see the "SSL" section of the ApacheProxy page for more information:
https://bitbucket.org/galaxy/**galaxy-central/wiki/Config/** ApacheProxy<https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy>
--nat
Sergei Ryazansky wrote:
Hi all, I would like to update the issue. I have found the following thread from the galaxy-dev list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html and according to the suggestion from it I have modified the UCSC_SITES in lib/galaxy/web/framework/__init__.py and 'sites' in lib/galaxy/security/__init__.py. Now these files contatin the url of our local mirror. After these changing the calling of display of bed file in local UCSC Genome Browser results in the following error message: "Unrecognized format line 1 of http://dmbcserv.dyndns.org/galaxy/root/display_as?id=436&display_app=ucsc&authz_method=display_at: You are not allowed to access this dataset. (note: chrom names are case sensitive)" You can check this on our public Galaxy mirror: http://dmbcserv.dyndns.org/galaxy. Have you any idea how to fix this?
Hi Sergei, It looks like this may be a bug with the external display authorization and the require_login feature. I'll take a look as soon as possible. --nate
2011/7/7 Sergei Ryazansky <s.ryazansky@gmail.com>
Hi Nate,
No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the mentioned above error.
06.07.2011 22:30, Nate Coraor пишет:
Sergei Ryazansky wrote:
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the "redirected to non-http(s): /root" error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance!
Hi Sergei,
If your Galaxy server is behind a proxy server serving via https, have you set the following header:
RequestHeader set X-URL-SCHEME https
Please see the "SSL" section of the ApacheProxy page for more information:
https://bitbucket.org/galaxy/**galaxy-central/wiki/Config/** ApacheProxy<https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy>
--nat
Hi, I also faced the same problem. I have a local galaxy and local ucsc genome browser mirror. The galaxy mirror is configured with the require_login equals to True. When I tried to display the data from galaxy to the local ucsc, I encountered the "redirected to non-http(s): /root" error as well. I have also followed the work around as described in the thread http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html, but I still encounter the "redirected to non-http(s): /root" error intermittently. Is there a fix or workaround to this problem that works? Thanks for your help. Best regards, Chee Seng, Chan -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Tuesday, August 16, 2011 3:49 AM To: Sergei Ryazansky Cc: Galaxy Dev Subject: Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy Sergei Ryazansky wrote:
Hi all, I would like to update the issue. I have found the following thread from the galaxy-dev list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html and according to the suggestion from it I have modified the UCSC_SITES in lib/galaxy/web/framework/__init__.py and 'sites' in lib/galaxy/security/__init__.py. Now these files contatin the url of our local mirror. After these changing the calling of display of bed file in local UCSC Genome Browser results in the following error message: "Unrecognized format line 1 of http://dmbcserv.dyndns.org/galaxy/root/display_as?id=436&display_app=ucsc&authz_method=display_at: You are not allowed to access this dataset. (note: chrom names are case sensitive)" You can check this on our public Galaxy mirror: http://dmbcserv.dyndns.org/galaxy. Have you any idea how to fix this?
Hi Sergei, It looks like this may be a bug with the external display authorization and the require_login feature. I'll take a look as soon as possible. --nate
2011/7/7 Sergei Ryazansky <s.ryazansky@gmail.com>
Hi Nate,
No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the mentioned above error.
06.07.2011 22:30, Nate Coraor пишет:
Sergei Ryazansky wrote:
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the "redirected to non-http(s): /root" error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance!
Hi Sergei,
If your Galaxy server is behind a proxy server serving via https, have you set the following header:
RequestHeader set X-URL-SCHEME https
Please see the "SSL" section of the ApacheProxy page for more information:
https://bitbucket.org/galaxy/**galaxy-central/wiki/Config/** ApacheProxy<https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy>
--nat
___________________________________________________________ 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/
CHAN Chee Seng wrote:
Hi,
I also faced the same problem.
I have a local galaxy and local ucsc genome browser mirror. The galaxy mirror is configured with the require_login equals to True. When I tried to display the data from galaxy to the local ucsc, I encountered the "redirected to non-http(s): /root" error as well.
I have also followed the work around as described in the thread http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html, but I still encounter the "redirected to non-http(s): /root" error intermittently.
Is there a fix or workaround to this problem that works?
Hi, Unfortunately, I haven't had a chance to look at this yet. I will try to do so within the next week. --nate
Thanks for your help.
Best regards, Chee Seng, Chan
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Tuesday, August 16, 2011 3:49 AM To: Sergei Ryazansky Cc: Galaxy Dev Subject: Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy
Sergei Ryazansky wrote:
Hi all, I would like to update the issue. I have found the following thread from the galaxy-dev list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html and according to the suggestion from it I have modified the UCSC_SITES in lib/galaxy/web/framework/__init__.py and 'sites' in lib/galaxy/security/__init__.py. Now these files contatin the url of our local mirror. After these changing the calling of display of bed file in local UCSC Genome Browser results in the following error message: "Unrecognized format line 1 of http://dmbcserv.dyndns.org/galaxy/root/display_as?id=436&display_app=ucsc&authz_method=display_at: You are not allowed to access this dataset. (note: chrom names are case sensitive)" You can check this on our public Galaxy mirror: http://dmbcserv.dyndns.org/galaxy. Have you any idea how to fix this?
Hi Sergei,
It looks like this may be a bug with the external display authorization and the require_login feature. I'll take a look as soon as possible.
--nate
2011/7/7 Sergei Ryazansky <s.ryazansky@gmail.com>
Hi Nate,
No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the mentioned above error.
06.07.2011 22:30, Nate Coraor пишет:
Sergei Ryazansky wrote:
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the "redirected to non-http(s): /root" error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance!
Hi Sergei,
If your Galaxy server is behind a proxy server serving via https, have you set the following header:
RequestHeader set X-URL-SCHEME https
Please see the "SSL" section of the ApacheProxy page for more information:
https://bitbucket.org/galaxy/**galaxy-central/wiki/Config/** ApacheProxy<https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy>
--nat
___________________________________________________________ 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:
___________________________________________________________ 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:
Hi Nate, Thanks for looking into this. I am wondering if you have the work around for this problem. Thanks so much. Best regards, Chee Seng -----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Wednesday, September 07, 2011 9:53 PM To: CHAN Chee Seng Cc: Galaxy Dev Subject: Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy CHAN Chee Seng wrote:
Hi,
I also faced the same problem.
I have a local galaxy and local ucsc genome browser mirror. The galaxy mirror is configured with the require_login equals to True. When I tried to display the data from galaxy to the local ucsc, I encountered the "redirected to non-http(s): /root" error as well.
I have also followed the work around as described in the thread http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html, but I still encounter the "redirected to non-http(s): /root" error intermittently.
Is there a fix or workaround to this problem that works?
Hi, Unfortunately, I haven't had a chance to look at this yet. I will try to do so within the next week. --nate
Thanks for your help.
Best regards, Chee Seng, Chan
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Tuesday, August 16, 2011 3:49 AM To: Sergei Ryazansky Cc: Galaxy Dev Subject: Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy
Sergei Ryazansky wrote:
Hi all, I would like to update the issue. I have found the following thread from the galaxy-dev list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html and according to the suggestion from it I have modified the UCSC_SITES in lib/galaxy/web/framework/__init__.py and 'sites' in lib/galaxy/security/__init__.py. Now these files contatin the url of our local mirror. After these changing the calling of display of bed file in local UCSC Genome Browser results in the following error message: "Unrecognized format line 1 of http://dmbcserv.dyndns.org/galaxy/root/display_as?id=436&display_app=ucsc&authz_method=display_at: You are not allowed to access this dataset. (note: chrom names are case sensitive)" You can check this on our public Galaxy mirror: http://dmbcserv.dyndns.org/galaxy. Have you any idea how to fix this?
Hi Sergei,
It looks like this may be a bug with the external display authorization and the require_login feature. I'll take a look as soon as possible.
--nate
2011/7/7 Sergei Ryazansky <s.ryazansky@gmail.com>
Hi Nate,
No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the mentioned above error.
06.07.2011 22:30, Nate Coraor пишет:
Sergei Ryazansky wrote:
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the "redirected to non-http(s): /root" error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance!
Hi Sergei,
If your Galaxy server is behind a proxy server serving via https, have you set the following header:
RequestHeader set X-URL-SCHEME https
Please see the "SSL" section of the ApacheProxy page for more information:
https://bitbucket.org/galaxy/**galaxy-central/wiki/Config/** ApacheProxy<https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy>
--nat
___________________________________________________________ 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:
___________________________________________________________ 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:
Hi Chee Seng, I created an issue at bitbucket so that everyone can track the progress for this issue. As of later on Friday 9/30, it was still open. https://bitbucket.org/galaxy/galaxy-central/issue/663/external-display-issue... Take care, Jen Galaxy team On 10/3/11 2:04 AM, CHAN Chee Seng wrote:
Hi Nate,
Thanks for looking into this. I am wondering if you have the work around for this problem. Thanks so much.
Best regards, Chee Seng
-----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Wednesday, September 07, 2011 9:53 PM To: CHAN Chee Seng Cc: Galaxy Dev Subject: Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy
CHAN Chee Seng wrote:
Hi,
I also faced the same problem.
I have a local galaxy and local ucsc genome browser mirror. The galaxy mirror is configured with the require_login equals to True. When I tried to display the data from galaxy to the local ucsc, I encountered the "redirected to non-http(s): /root" error as well.
I have also followed the work around as described in the thread http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html, but I still encounter the "redirected to non-http(s): /root" error intermittently.
Is there a fix or workaround to this problem that works?
Hi,
Unfortunately, I haven't had a chance to look at this yet. I will try to do so within the next week.
--nate
Thanks for your help.
Best regards, Chee Seng, Chan
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Tuesday, August 16, 2011 3:49 AM To: Sergei Ryazansky Cc: Galaxy Dev Subject: Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy
Sergei Ryazansky wrote:
Hi all, I would like to update the issue. I have found the following thread from the galaxy-dev list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html and according to the suggestion from it I have modified the UCSC_SITES in lib/galaxy/web/framework/__init__.py and 'sites' in lib/galaxy/security/__init__.py. Now these files contatin the url of our local mirror. After these changing the calling of display of bed file in local UCSC Genome Browser results in the following error message: "Unrecognized format line 1 of http://dmbcserv.dyndns.org/galaxy/root/display_as?id=436&display_app=ucsc&authz_method=display_at: You are not allowed to access this dataset. (note: chrom names are case sensitive)" You can check this on our public Galaxy mirror: http://dmbcserv.dyndns.org/galaxy. Have you any idea how to fix this?
Hi Sergei,
It looks like this may be a bug with the external display authorization and the require_login feature. I'll take a look as soon as possible.
--nate
2011/7/7 Sergei Ryazansky<s.ryazansky@gmail.com>
Hi Nate,
No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the mentioned above error.
06.07.2011 22:30, Nate Coraor пишет:
Sergei Ryazansky wrote:
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the "redirected to non-http(s): /root" error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance!
Hi Sergei,
If your Galaxy server is behind a proxy server serving via https, have you set the following header:
RequestHeader set X-URL-SCHEME https
Please see the "SSL" section of the ApacheProxy page for more information:
https://bitbucket.org/galaxy/**galaxy-central/wiki/Config/** ApacheProxy<https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy>
--nat
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
participants (4)
-
CHAN Chee Seng -
Jennifer Jackson -
Nate Coraor -
Sergei Ryazansky