Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

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&am...;. If you just go to http:// galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%2... <http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text&am... 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(a)fmi.ch&gt; 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 > > > > http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text&am... > > > > 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(a)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/c49e7803fa1814abd04afb26b5... > > ) 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/ > > >