Execute command once job has completed

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Execute command once job has completed

evan clark
Is there a method to setup a command to run depending on the filetype of
a job. Essentially I want to setup a task where everytime a bedgraph
file is generated it will either automatically start a new job and
convert it to bigwig or, within the same job file it will convert the
bedgraph to bigwig.
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Re: Execute command once job has completed

Peter Cock
It depends on what you mean by automatic. You could
create a Galaxy Workflow where a tool is run which
generates the bedgraph file, and then as the next
step it is converted to bigwig.

For this specific task, it might be possible to exploit
the Galaxy datatype definition for bedgraph to allow
automatic conversion to bigwig - is this working for you?

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml

Peter

On Tue, Feb 28, 2017 at 4:47 PM, evan clark <[hidden email]> wrote:

> Is there a method to setup a command to run depending on the filetype of a
> job. Essentially I want to setup a task where everytime a bedgraph file is
> generated it will either automatically start a new job and convert it to
> bigwig or, within the same job file it will convert the bedgraph to bigwig.
> ___________________________________________________________
> 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:
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>
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Re: Execute command once job has completed

Peter Cock
I do not believe that is possible (nor desirable in general,
not everyone will need or want the converted file and the
overhead that comes with creating and storing it).

What do you want to do with the bigwig file, and is the
automatic conversion working for you? i.e. If you have
tool X in Galaxy which wants an bigwig input file, does
Galaxy offer an automated conversion of your bedgraph
file as an input in the drop down file list?

Peter


On Tue, Feb 28, 2017 at 5:27 PM, evan clark <[hidden email]> wrote:

> By automatic I mean that once any bedgraph file is finished writing it will
> automatically run the convert to bigwig command
>
>
> Peter Cock
> February 28, 2017 12:21 PM
> It depends on what you mean by automatic. You could
> create a Galaxy Workflow where a tool is run which
> generates the bedgraph file, and then as the next
> step it is converted to bigwig.
>
> For this specific task, it might be possible to exploit
> the Galaxy datatype definition for bedgraph to allow
> automatic conversion to bigwig - is this working for you?
>
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
>
> Peter
> evan clark
> February 28, 2017 11:47 AM
> Is there a method to setup a command to run depending on the filetype of a
> job. Essentially I want to setup a task where everytime a bedgraph file is
> generated it will either automatically start a new job and convert it to
> bigwig or, within the same job file it will convert the bedgraph to bigwig.
>
>
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