Hey Michael,
I know there is a lot of interest in this, but these sorts of things
are not possible with Galaxy workflows at this time. If you want the
traceibility and UI for viewing results provided by Galaxy - you could
consider driving tools externally via the API - at that point though
the
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Hi Michael,
I, too, would love to have conditionals and loops, however may want to
consider the following approach:
Instead of splitting the web service submission, check for results, and
download of results into three steps, make it a single
While I agree that would work, the tool I’m working with generates tools for
web operations in a generic fashion. That is, you provide it a WDSL and a list
of operations you want from that WSDL, and then tool XML files are generated
for each of those operations.
Sincerely,
Michael E.
On Thu, Mar 6, 2014 at 2:12 PM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
While I agree that would work, the tool I'm working with generates
tools for web operations in a generic fashion. That is, you provide
it a WDSL and a list of operations you want from that WSDL, and
then tool
The tool is generic. This means that it is supposed to work (and does work)
with any WSDL. In the described use case, one of the operations/“generated
tools already serves as a polling tool: it takes a unique id and requests a
result from the web service, then the web service either returns the
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We're not suggesting adding a polling tool; instead the suggestion was
that your WSDL tool generator generate the XML tool definition and a
wrapper script.
That wrapper script would handle whatever WSDL operation it was created
for, polling, and
I’m sorry for the confusion. These really are three different operations that
handled by three different web service operations with the web service. Other
WSDLs might have similar operations, but the process might be different. There
is no generic way to do what you just described.
I remember this being mentioned in a project called Tavaxy
http://www.biomedcentral.com/1471-2105/13/77, but it's a separate piece of
software (using Galaxy) and I don't know if it's been updated in a while so
it may not be as useful for you. Not sure if anybody else had any
experience with it?
Is there a way to have conditionals and loops for the various steps in a Galaxy
workflow?
For example, a conditional might be used to branch to various steps based on
the previous steps. Also, a step may need to be repeated until it produces a
particular output.
Here is an actual use case:
Hey Eric,
Thanks for thinking through some of those details. I don't know if
this is an extension of that or an alternative to that - but the
Galaxy tool shed has some support for workflows and stored these in a
VCS repository (mercurial). Augmenting that to support a sort of
one-click (or
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Hi Peter,
Please bear with me, I'm mostly tossing these ideas out for my
benefit/to spawn discussion on how one might implement this. This was
originally a short email before I figured out how much work would be
involved...
Upon cursory inspection I
Hi John,
I've just tried a workflow using my MIRA4 de novo wrapper:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
To keep it simple, in this example I just had two input FASTQ
files, the forward and reverse files for paired end MiSeq data.
This seemed to work fine for
I am pretty confident this worked at some point, this is potentially a
regression of some kind (or I am crazy person). I will try to find
time to take a closer look.
I have created a Trello card for this:
https://trello.com/c/9knsbvmx
Sorry about that!
-John
On Wed, Oct 30, 2013 at 12:35 PM,
On Wed, Oct 30, 2013 at 6:02 PM, John Chilton chil...@msi.umn.edu wrote:
I am pretty confident this worked at some point, this is potentially a
regression of some kind (or I am crazy person). I will try to find
time to take a closer look.
OK, likewise - I'll try to put together a reproducible
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I'm working with a number of people in my department to develop a single
workflow that will be used for a course we teach. So far I've found that
sharing a workflow with individual users/roles isn't very optimal.
They email me with changes they'd like
Hi Eric,
I've being pondering this too - it can easily get very complicated
with multiple copies of a workflow with minor variations.
I agree that read only sharing makes sense as a short term
goal, but I see two variants being useful here - an read only
snapshot copy from the instant it was
Subject: [galaxy-dev] workflows stop prematurely
Hi All
On my local install of galaxy I'm having problems executing workflows. I will
upload data into a new history and then select to run a saved workflow. This
initiates fine but, after the completion of a variable number of steps, the
workflow
Hi All
On my local install of galaxy I'm having problems executing workflows. I will
upload data into a new history and then select to run a saved workflow. This
initiates fine but, after the completion of a variable number of steps, the
workflow just stops after the successful completion
Hi,
I've put together some exempels for activating and using the api. You can find
them here:
http://geertvandeweyer.zymichost.com/index.php?page=readid=29
Best regards,
Geert vandeweyer
Op 16-jan.-2013 om 02:52 heeft neil.burd...@csiro.au het volgende geschreven:
Hi
Sorry if these
Neil,
.../api/workflows is not a path in the galaxy directory, but a URL
that you should access over HTTP. For example, if you login to Galaxy
Test, and then access https://test.g2.bx.psu.edu/api/workflows you
will get a json dict of all of your workflows, including the workflow
id that you are
Hi
Sorry if these questions are obvious but I just don't know how to find the
answers.
I'm trying to get one of the API examples to work in
http://wiki.galaxyproject.org/Learn/API/Examples .
I've got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in
the examples). I've
Hello,
after commit 29680fa5c35e we are not able to open workflows anymore.
The error message is:
TypeError: mako.template.Template object at 0x6dc8e10 is not JSON
serializable
And the problematic changeset is here:
Fixed in 4d22e26e595a
Thanks,
J.
On Aug 8, 2012, at 6:05 AM, Björn Grüning wrote:
Hello,
after commit 29680fa5c35e we are not able to open workflows anymore.
The error message is:
TypeError: mako.template.Template object at 0x6dc8e10 is not JSON
serializable
And the problematic
Fixed on trunk, thanks for reporting!
K
On Thu, Jul 21, 2011 at 12:41 PM, Edward Kirton eskir...@lbl.gov wrote:
URL: https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8
Module paste.exceptions.errormiddleware:*143* in __call__
Module paste.debug.prints:*98* in __call__
Module
yup, works. thanks for the prompt reply
On Thu, Jul 21, 2011 at 10:15 AM, Kanwei Li kan...@gmail.com wrote:
Fixed on trunk, thanks for reporting!
K
On Thu, Jul 21, 2011 at 12:41 PM, Edward Kirton eskir...@lbl.gov wrote:
URL: https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8
Hi everyone
First let me thank all the Team Galaxy, the conference was really great.
Kanwei asked me to send the tool I told him about. It's one of these
tools for which you can't know the exact number of output datasets
before tool run. Here are the files. It's really simple actually, but it
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