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
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
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
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
The correct link is this: http://galaxy-dev.fmi.ch/tool_
runner/biomart?type=text=Homo%20sapiens%20genes%20%
28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/
7ee294b9ae51a27f1e7ed96e712c5792?
On Wed, Jun 8, 2016 at 11:33 AM Martin Čech wrote:
> This looks like an
This looks like an Ensembl problem, because they are prefixing the redirect
url with "http://www.ensembl.org/
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:
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"] =
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
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
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
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