Hi Geert,
thanks for your reply. Unfortunately it is not feasible for us to use a script
outside Galaxy. As long as no official feature for Galaxy is released I will
work on a script which will execute workflows via the API and add this script
as a tool into Galaxy.
Cheers,
Sascha
Hi,
I've also thought about that approach, but the problem here is that I
don't find a way to request the users api key from a tool-xml. So you
would have to hard-code an api key in the tool configuration. Or is
there a way to request a user's api key from a galaxy-tool. That would
also
Hi!
Yeah, it seems that there is now way to request the API key automatically.
One simple apporach would be an extra text input field where the user has
to enter his or her API key.
In my use case it will be better to use a file for mapping $__user_id__ -
api_key.
We run Galaxy only
Hi Sascha and Geert,
A quick and dirty way to get the API key during tool execution would be
something like:
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
Of course, it would be better if there were a more straightforward way to
access the key. It would also be a good idea to add
Hello Sabbirjoy,
In order to use the public Galaxy tool sheds you need to be running the tip
from Galaxy central. This will change as of the next Galaxy release, which I
believe is scheduled soon. After the next release, the tool sheds will follow
the Galaxy dist repository.
Greg Von Kuster
Hell yeah Dan!
this will make things a lot easier and is a good starting point.
Thank you very very much!
Cheers,
Sascha
Original Message
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Subject:
Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows
Sent:
Donnerstag, 19. Juli
Hi,
I am using your program from my home computer (portable computer with a small
screen). I can do all the lefse analysis succesfully (everything is green) but
cannot open the results- I click on the results but they do not open. when I
click on the 'eye' icon I do get a file, but I don't
Hi all,
I was wondering how to upload several files at a time, without clicking on
every checkbox to upload file with FTP. Like creating an select all option,
is it possible?
Best regards
Mish
JavaScript logs are found in the Web browser. For Safari/Chrome, see the View
-- Developer -- JavaScript console option; for Firefox, see Tools -- Web
Developer -- Web Console.
The fact that the Paster log isn't showing errors is problematic. Are there
certain scenarios where Trackster/Galaxy
HI!
I'am usig Galaxy-dist.
SO I have done the test again, I did a simple scrolling to visualize by the
Trackster the different chromosome regions and then the galaxy crashed
suddenly.
Here Above what java script log looks :
Hi all.
Is there a way to get the job working directory or the job id from the
implementation of exec_before_job hook?
This hook function produces a file and I would like to store it in a job
working directory.
Thanks.
Roberto
___
Please
Greetings all,
I'm trying to build out a Galaxy workflow to support trinity rna-seq
de novo assembly and all the various downstream analyses. For the
initial trinity de novo assembly, I took Jeremy's initial workflow and
tweaked it to work with the latest release - and submitted it to the
galaxy
change your tool to use explicitly named output folder and files
bash mytool.sh $input $output1.extra_files_path $output1 $output2
where $output1.extra_files_path will be a folder (e.g. working dir)
$output1, $output2, etc. are files that are to be brought into your history
in galaxy, to be
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