How to install Charts in command line ?

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How to install Charts in command line ?

Steven Shen
Hi all,

Cytoscape, Bar diagram(NVD3), Horizontal(NVD3) , and other NVD3  visualization tools are working good on my local galaxy  except  the jqplots, such as Box plot, Discrete Histogram,   with error "This visualization requires the 'charts' tool. Please make sure it is installed." It seems i need to install Charts first.

Actually Charts could be installed from the Tool Shed through the Admin Interface, but it failed sometimes as the bad network. so is there any doc about installing Charts/tools through command line?

Thank you.
Steven

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Re: How to install Charts in command line ?

Aysam Guerler
Hey,

There is no documentation for this but it is possible. You need to install R and two R libraries (getopt, Matrix) in order to execute the charts R-script. Once R is configured you can add the charts tool to the tools directory and update your config/tool_conf.xml file accordingly before restarting your local instance.

Having said this, can you specify in more detail why the tool installation fails. Can you install other tools from the toolshed without problems?

I hope this helps.

Thanks,
Sam

On Mon, Jul 17, 2017 at 9:53 AM, Steven Shen <[hidden email]> wrote:
Hi all,

Cytoscape, Bar diagram(NVD3), Horizontal(NVD3) , and other NVD3  visualization tools are working good on my local galaxy  except  the jqplots, such as Box plot, Discrete Histogram,   with error "This visualization requires the 'charts' tool. Please make sure it is installed." It seems i need to install Charts first.

Actually Charts could be installed from the Tool Shed through the Admin Interface, but it failed sometimes as the bad network. so is there any doc about installing Charts/tools through command line?

Thank you.
Steven

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Re: How to install Charts in command line ?

James Taylor-2
Would it make sense to change these tools to conda dependencies?
r-getopt and r-getopt are already in conda-forge so should be an easy
change.

On Mon, Jul 17, 2017 at 12:38 PM, Aysam Guerler <[hidden email]> wrote:

> Hey,
>
> There is no documentation for this but it is possible. You need to install R
> and two R libraries (getopt, Matrix) in order to execute the charts
> R-script. Once R is configured you can add the charts tool to the tools
> directory and update your config/tool_conf.xml file accordingly before
> restarting your local instance.
>
> Having said this, can you specify in more detail why the tool installation
> fails. Can you install other tools from the toolshed without problems?
>
> I hope this helps.
>
> Thanks,
> Sam
>
> On Mon, Jul 17, 2017 at 9:53 AM, Steven Shen <[hidden email]> wrote:
>>
>> Hi all,
>>
>> Cytoscape, Bar diagram(NVD3), Horizontal(NVD3) , and other NVD3
>> visualization tools are working good on my local galaxy  except  the
>> jqplots, such as Box plot, Discrete Histogram,   with error "This
>> visualization requires the 'charts' tool. Please make sure it is installed."
>> It seems i need to install Charts first.
>>
>> Actually Charts could be installed from the Tool Shed through the Admin
>> Interface, but it failed sometimes as the bad network. so is there any doc
>> about installing Charts/tools through command line?
>>
>> Thank you.
>> Steven
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/
>
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
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Re: How to install Charts in command line ?

Aysam Guerler
I agree, it should be straightforward. I will look into it.

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Re: How to install Charts in command line ?

Steven Shen
Thank you very much. The instability network in our  company leads to Charts installation fail, but now it can be installed successfully through Tool Shed.

If someone want to install some tools through command line manually, it may be a few complex for the tool dependents somethimes.

2017-07-18 2:26 GMT+08:00 Aysam Guerler <[hidden email]>:
I agree, it should be straightforward. I will look into it.


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