[galaxy-dev] Xenopus genome

Dear Galaxy team, First, thanks for your great work! I want to use Bowtie2 to align ChIPseq data to the Xenopus laevis genome. However, It's not listed. The tool said that if the desired genome is not in the list to contact the galaxy team, so here I am :) Could you add this? Thanks! Stefan _

[galaxy-dev] Using session parameters in Galaxy tools

Is it possible to access session parameters and use them in Galaxy tool wrappers? If so, how? I am integrating Galaxy with a local system, and I need the current session ID to be able to access user and session-specific data. I am already getting the user email as $__user_email__ (from https://wiki

Re: [galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?

Thanks Martin! With your hint and the example from graphviz.mako I was able to get this to work. Cheers, Malcolm On Wednesday, June 08, 2016 03:23:31 PM Martin Čech wrote: Hello Malcolm, encoded_id is a database row id that has been ran through this method (https://github.com/galaxyproj

[galaxy-dev] Any way to prime the value of a tool text field parameter dynamically?

I have a need to have the default value of a text parameter : Set dynamically, as powered by say a call to a function in , much like a dynamic_options="get_rule_section(recipe_file)" call. Has anyone done that somehow without hacking Galaxy code? A user can then edit the text. The default

Re: [galaxy-dev] not sure what I can do about this...

Hey guys, I successfully fixed my problem. Here's the solution if you would like to know: 1. download zlib-1.2.8.tar.gz 2. ./configure --prefix=/usr/local/zlib-1.2.8 3. make 4. make install 5. add the following in the file config/local_env.sh export LD_LIBRARY_PATH=/usr/local/zlib-1.2.8$

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

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 wrote: > This looks like an Ensembl problem,

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/

Re: [galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?

Hello Malcolm, encoded_id is a database row id that has been ran through this method ( https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__init__.py#L46) using the 'secret' from galaxy.ini config. You should be able to do something like this in the mako: ${trans.security.e

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

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/biomar

[galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?

I'm really close to having a way to visualize radiological images in Galaxy, but need help in getting past the final hurdle. In the mako file, I can see how to pass parameters to the javascript that does the visualization. It's expecting a URL to the dataset, like: params["images"] = ["/datas

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

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 wrote: > Hi all > > Please allow me to come back to this old problem: > > On usegalaxy.org, the tool is

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

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/c49e7803fa1814abd04afb26b54965fb7af612ac ) and it seems to work, i.e stuff is sent to usegal

Re: [galaxy-dev] Deploying custom genome in Galaxy for use with ANNOVAR

Hello David I don't think it will answer all your questions, however: I wrote up my experiences with installing ANNOVAR in Galaxy last year which might be useful as a starting point: http://galacticengineer.blogspot.co.uk/2015/03/installing-annovar-in-galaxy.html As I recall all the database