conditions within workflows

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conditions within workflows

Olivia Doppelt
Dear developpers,

I have a question concerning the insertion of conditions inside workflows ?

Here, at the pasteur Institute, we would like to use galaxy to create a
microbiome analysis workflow. However, it requires at least 10 different
tools which may be or may not be used in several cases.

For the moment, all I see is to create a giant wrapper for this workflow
but it would be loosing the great interest of galaxy.

I see on bitbucket that there is a branch on galaxy-central named
"galaxy-central-conditional-toolbox-elements" are there new elements
since february ?

Best regards,

--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur

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Re: conditions within workflows

Dannon Baker-2
Hi Olivia,

Currently it's not possible to have conditional job execution in workflows, though this is definitely something we've talked about adding.

The conditional toolbox element repository that you found is actually some of John's work on conditionally having tools in the toolbox, not for making run-time decisions in workflows.  This is an active pull request (https://bitbucket.org/galaxy/galaxy-central/pull-request/160) that I hope to have time to review soon.

-Dannon

On Tue, May 7, 2013 at 10:02 AM, Olivia Doppelt <[hidden email]> wrote:
Dear developpers,

I have a question concerning the insertion of conditions inside workflows ?

Here, at the pasteur Institute, we would like to use galaxy to create a microbiome analysis workflow. However, it requires at least 10 different tools which may be or may not be used in several cases.

For the moment, all I see is to create a giant wrapper for this workflow but it would be loosing the great interest of galaxy.

I see on bitbucket that there is a branch on galaxy-central named "galaxy-central-conditional-toolbox-elements" are there new elements since february ?

Best regards,

--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/