Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

[Jennifer Jackson]

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-when-running-galaxy

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:n...@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-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@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


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




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Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

[CHAN Chee Seng]

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:n...@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-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@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 
> > 
> > > 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/A

Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

[Nate Coraor]

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-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@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 
> > 
> > > 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
> > >>
> > >
> ___
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> and other Galaxy lists, please use the interface at:
> 
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> 
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> 
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Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

[CHAN Chee Seng]

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-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@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 
> 
> > 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
> >>
> >
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___
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and other Galaxy lists, please use the interface at:

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Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

[Nate Coraor]

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 
> 
> > 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
> >>
> >
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Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

[Sergei Ryazansky]

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 

> 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
>>
>
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Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

[Sergei Ryazansky]

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

___
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/

Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

[Nate Coraor]

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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