How to replace 'BioMart Central server' in the "Get Data" tools ?
Hi As you probably know, the central BioMart server is currently unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get Data -> BioMart Central server" tool in our local Galaxy installation does not work anymore - well, this is also the case on usegalaxy.org. We can easily switch the tool to point to a different Mart server, i.e.: Change: <inputs action="http://www.biomart.org/biomart/martview" .... to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" .... However, we would like to switch to the ensembl Mart server: http://www.ensembl.org/biomart/martview It looks like the ensembl Mart server is nowadays embedded in the ensembl web site, and the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found". Unfortunately, I am not that savvy about the inner works of the ensembl web site anymore ;) Has anyone else looked into this problem and found already a solution? Thank you very much for any help Hans-Rudolf
Hi all Please allow me to come back to this old problem: On usegalaxy.org, the tool is now pointing to http://www.ensembl.org/biomart/martview (see also: https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b5496... ) and it seems to work, i.e stuff is sent to usegalaxy.org. If I try to do the same on our local galaxy server, I still run into the same problem as last November: the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found". Is there anything else, I need to change? Thank you very much for your help Hans-Rudolf On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote:
Hi
As you probably know, the central BioMart server is currently unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get Data -> BioMart Central server" tool in our local Galaxy installation does not work anymore - well, this is also the case on usegalaxy.org.
We can easily switch the tool to point to a different Mart server, i.e.:
Change: <inputs action="http://www.biomart.org/biomart/martview" ....
to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" ....
However, we would like to switch to the ensembl Mart server:
http://www.ensembl.org/biomart/martview
It looks like the ensembl Mart server is nowadays embedded in the ensembl web site, and the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found". Unfortunately, I am not that savvy about the inner works of the ensembl web site anymore ;)
Has anyone else looked into this problem and found already a solution?
Thank you very much for any help
Hans-Rudolf
Hello Hans-Rudolf, What version of Galaxy are you using? Can you please share a specific URL you were sent to that returns a 404? thanks M. On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi all
Please allow me to come back to this old problem:
On usegalaxy.org, the tool is now pointing to http://www.ensembl.org/biomart/martview (see also:
https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b5496... ) and it seems to work, i.e stuff is sent to usegalaxy.org.
If I try to do the same on our local galaxy server, I still run into the same problem as last November: the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found".
Is there anything else, I need to change?
Thank you very much for your help Hans-Rudolf
On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote:
Hi
As you probably know, the central BioMart server is currently unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get Data -> BioMart Central server" tool in our local Galaxy installation does not work anymore - well, this is also the case on usegalaxy.org.
We can easily switch the tool to point to a different Mart server, i.e.:
Change: <inputs action="http://www.biomart.org/biomart/martview" ....
to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" ....
However, we would like to switch to the ensembl Mart server:
http://www.ensembl.org/biomart/martview
It looks like the ensembl Mart server is nowadays embedded in the ensembl web site, and the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found". Unfortunately, I am not that savvy about the inner works of the ensembl web site anymore ;)
Has anyone else looked into this problem and found already a solution?
Thank you very much for any help
Hans-Rudolf
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Martin we are still on "15.10" (minor version "2") However, I see the same issues on other public galaxy server which are already on 16.04 http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%20genes%20%28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1&resultsButton=1 Hans-Rudolf On 06/08/2016 04:36 PM, Martin Čech wrote:
Hello Hans-Rudolf,
What version of Galaxy are you using? Can you please share a specific URL you were sent to that returns a 404?
thanks
M.
On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi all
Please allow me to come back to this old problem:
On usegalaxy.org <http://usegalaxy.org>, the tool is now pointing to http://www.ensembl.org/biomart/martview (see also: https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b5496... ) and it seems to work, i.e stuff is sent to usegalaxy.org <http://usegalaxy.org>.
If I try to do the same on our local galaxy server, I still run into the same problem as last November: the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found".
Is there anything else, I need to change?
Thank you very much for your help Hans-Rudolf
On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote: > Hi > > As you probably know, the central BioMart server is currently > unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get > Data -> BioMart Central server" tool in our local Galaxy installation > does not work anymore - well, this is also the case on usegalaxy.org <http://usegalaxy.org>. > > > We can easily switch the tool to point to a different Mart server, i.e.: > > Change: <inputs action="http://www.biomart.org/biomart/martview" .... > > to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" .... > > > However, we would like to switch to the ensembl Mart server: > > http://www.ensembl.org/biomart/martview > > > It looks like the ensembl Mart server is nowadays embedded in the > ensembl web site, and the requests are not send to Galaxy, but end up on > the ensembl web page, where they cause a "Error 404 - Page not found". > Unfortunately, I am not that savvy about the inner works of the ensembl > web site anymore ;) > > > Has anyone else looked into this problem and found already a solution? > > Thank you very much for any help > > > Hans-Rudolf > > ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
This looks like an Ensembl problem, because they are prefixing the redirect url with "http://www.ensembl.org/ <http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%20genes%20%28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1&resultsButton=1>". If you just go to http:// galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%20genes%20%28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1&resultsButton=1 <http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%20genes%20%28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1&resultsButton=1> it will most probably work. They might be whitelisting usegalaxy.org to not add prefix, or some other bug, I will try contacting them, thank you for the report. Martin On Wed, Jun 8, 2016 at 11:19 AM Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Martin
we are still on "15.10" (minor version "2")
However, I see the same issues on other public galaxy server which are already on 16.04
Hans-Rudolf
On 06/08/2016 04:36 PM, Martin Čech wrote:
Hello Hans-Rudolf,
What version of Galaxy are you using? Can you please share a specific URL you were sent to that returns a 404?
thanks
M.
On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi all
Please allow me to come back to this old problem:
On usegalaxy.org <http://usegalaxy.org>, the tool is now pointing to http://www.ensembl.org/biomart/martview (see also:
https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b5496...
) and it seems to work, i.e stuff is sent to usegalaxy.org <http://usegalaxy.org>.
If I try to do the same on our local galaxy server, I still run into
the
same problem as last November: the requests are not send to Galaxy,
but
end up on the ensembl web page, where they cause a "Error 404 - Page
not
found".
Is there anything else, I need to change?
Thank you very much for your help Hans-Rudolf
On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote: > Hi > > As you probably know, the central BioMart server is currently > unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get > Data -> BioMart Central server" tool in our local Galaxy
installation
> does not work anymore - well, this is also the case on usegalaxy.org <http://usegalaxy.org>. > > > We can easily switch the tool to point to a different Mart server, i.e.: > > Change: <inputs action="http://www.biomart.org/biomart/martview"
....
> > to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" .... > > > However, we would like to switch to the ensembl Mart server: > > http://www.ensembl.org/biomart/martview > > > It looks like the ensembl Mart server is nowadays embedded in the > ensembl web site, and the requests are not send to Galaxy, but end up on > the ensembl web page, where they cause a "Error 404 - Page not found". > Unfortunately, I am not that savvy about the inner works of the ensembl > web site anymore ;) > > > Has anyone else looked into this problem and found already a solution? > > Thank you very much for any help > > > Hans-Rudolf > > ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
The correct link is this: http://galaxy-dev.fmi.ch/tool_ runner/biomart?type=text&name=Homo%20sapiens%20genes%20% 28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/ 7ee294b9ae51a27f1e7ed96e712c5792? On Wed, Jun 8, 2016 at 11:33 AM Martin Čech <marten@bx.psu.edu> wrote:
This looks like an Ensembl problem, because they are prefixing the redirect url with "http://www.ensembl.org/ <http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%20genes%20%28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1&resultsButton=1>". If you just go to http:// galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%20genes%20%28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1&resultsButton=1 <http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%20genes%20%28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1&resultsButton=1> it will most probably work.
They might be whitelisting usegalaxy.org to not add prefix, or some other bug, I will try contacting them, thank you for the report.
Martin
On Wed, Jun 8, 2016 at 11:19 AM Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Martin
we are still on "15.10" (minor version "2")
However, I see the same issues on other public galaxy server which are already on 16.04
Hans-Rudolf
On 06/08/2016 04:36 PM, Martin Čech wrote:
Hello Hans-Rudolf,
What version of Galaxy are you using? Can you please share a specific URL you were sent to that returns a 404?
thanks
M.
On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi all
Please allow me to come back to this old problem:
On usegalaxy.org <http://usegalaxy.org>, the tool is now pointing to http://www.ensembl.org/biomart/martview (see also:
https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b5496...
) and it seems to work, i.e stuff is sent to usegalaxy.org <http://usegalaxy.org>.
If I try to do the same on our local galaxy server, I still run
into the
same problem as last November: the requests are not send to Galaxy,
but
end up on the ensembl web page, where they cause a "Error 404 -
Page not
found".
Is there anything else, I need to change?
Thank you very much for your help Hans-Rudolf
On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote: > Hi > > As you probably know, the central BioMart server is currently > unavailable (see: http://www.biomart.org/notice.html). Hence,
the
"Get > Data -> BioMart Central server" tool in our local Galaxy
installation
> does not work anymore - well, this is also the case on usegalaxy.org <http://usegalaxy.org>. > > > We can easily switch the tool to point to a different Mart server, i.e.: > > Change: <inputs action="http://www.biomart.org/biomart/martview"
....
> > to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" .... > > > However, we would like to switch to the ensembl Mart server: > > http://www.ensembl.org/biomart/martview > > > It looks like the ensembl Mart server is nowadays embedded in the > ensembl web site, and the requests are not send to Galaxy, but end up on > the ensembl web page, where they cause a "Error 404 - Page not found". > Unfortunately, I am not that savvy about the inner works of the ensembl > web site anymore ;) > > > Has anyone else looked into this problem and found already a solution? > > Thank you very much for any help > > > Hans-Rudolf > > ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Hans-Rudolf Hotz -
Martin Čech