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
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
processed by CONSOLIDATE
Subject:
Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows
Sent:
Donnerstag, 19. Juli
Hi Dev-Team,
are you planning or maybe working on an update which enables the
possiblilty to run workflows in batch mode with paired end data?
Cheers,
Sascha
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Hi,
In case you'd be interested: we use a script that creates interlaced
data of paired end data. We run this outside galaxy on groups of
samples ordered in directories at once. We then import the interlaced
data into galaxy, enabling batch workflow. The first step of the
workflow is a
But this only works if you have a single dataset (such as a BAM file) for each
workflow to run on.
If you have pairs of files (such as paired end FASTQ files, not an uncommon
workflow nowadays :) ) you need to resort to using the API, since there is no
support for paired end sequencing in
In your workflows, are you using Input Dataset steps? Galaxy uses these
steps to know how to map datasets to do special things like this. If you're
not currently using them, just open the workflow editor and add input dataset
steps (it's at the very bottom of the tool list) connected to the
Hello Dannon
Could it be possible to have the input dataset's display name appended
to the new history's name instead of plain numbers when the Send
results in a new history option is checked?
This new feature is indeed very useful (thanks a million for it) but
the numbered suffixes
Thanks for the suggestion, I like that! I'll make the change shortly.
-Dannon
On Feb 7, 2012, at 8:03 AM, Louise-Amélie Schmitt wrote:
Hello Dannon
Could it be possible to have the input dataset's display name appended to the
new history's name instead of plain numbers when the Send
Hi All,
I'm looking to batch process 40 large data sets with the same galaxy
workflow.
This obviously can be done in a brute-force manual manner.
However, is there a better way to schedule/invoke these jobs in batch
1) from the UI with a plugin
2) command-line
3) web-service
Thanks in advance
Hi Dave,Yes, galaxy's standard run-workflow dialog has a feature where you can select multiple datasets as input for a single "Input Dataset" step. To do this, click the icon referenced by the tooltip in the screenshot below to select multiple files. All parameters remain static between executions
Thank you Dannon. That is helpful.
What if I need to specify multiple inputs per run (i.e. .csfasta + .qual
file)?
-Dave
On Mon, Feb 6, 2012 at 1:27 PM, Dannon Baker dannonba...@me.com wrote:
Hi Dave,
Yes, galaxy's standard run-workflow dialog has a feature where you can
select multiple
This method only works for single inputs at the moment, though eventually it'd
be nice to allow pairing. Another option for you would be to use the workflows
API, with which you can definitely specify multiple inputs. See
workflow_execute.py in the scripts/api folder of your galaxy
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