> I was wondering if it is possible to activate CytoscapeRPC when > starting Cytoscape through the command line?
> Many thanks.
> Best,
> -- > You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group. > To post to this group, send email to cytoscape-discuss@googlegroups.com. > To unsubscribe from this group, send email to cytoscape-discuss+unsubscribe@googlegroups.com. > For more options, visit this group at http://groups.google.com/group/cytoscape-discuss?hl=en.
Well it’s not exactly what I want, because I would like to start
Cytoscape remotely without any GUI interface and start CytoscapeRPC
automatically to establish a connection with my script in python.
Though, it’s fine I made the change in CytoscapeRPC source code and
built it and then added the jar to the plugins folder in Cytoscape. It
worked :)
Thanks.
Cheers,
On Feb 20, 11:19 pm, Paul Shannon <paul.thurmond.shan...@gmail.com>
wrote:
> You can setup CyRPC so that it auto-starts on every subsequent Cytoscape session.
> Go to Plugins->CytoscapeRPC->Settings and click "Auto Start"
> I hope this helps!
> - Paul
> On Feb 20, 2012, at 5:02 AM, Emanuel wrote:
> > Hi,
> > I was wondering if it is possible to activate CytoscapeRPC when
> > starting Cytoscape through the command line?
> > Many thanks.
> > Best,
> > --
> > You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group.
> > To post to this group, send email to cytoscape-discuss@googlegroups.com.
> > To unsubscribe from this group, send email to cytoscape-discuss+unsubscribe@googlegroups.com.
> > For more options, visit this group athttp://groups.google.com/group/cytoscape-discuss?hl=en.
On Tuesday, February 21, 2012 8:36:31 AM UTC-5, Emanuel wrote:
> Hi Paul,
> Many thanks for your reply.
> Well it’s not exactly what I want, because I would like to start > Cytoscape remotely without any GUI interface and start CytoscapeRPC > automatically to establish a connection with my script in python.
> Though, it’s fine I made the change in CytoscapeRPC source code and > built it and then added the jar to the plugins folder in Cytoscape. It > worked :)
> Thanks.
> Cheers,
> On Feb 20, 11:19 pm, Paul Shannon <paul.thurmond.shan...@gmail.com> > wrote: > > Hi Emmanuel,
> > You can setup CyRPC so that it auto-starts on every subsequent Cytoscape > session. > > Go to Plugins->CytoscapeRPC->Settings and click "Auto Start"
> > I hope this helps!
> > - Paul
> > On Feb 20, 2012, at 5:02 AM, Emanuel wrote:
> > > Hi,
> > > I was wondering if it is possible to activate CytoscapeRPC when > > > starting Cytoscape through the command line?
> > > Many thanks.
> > > Best,
> > > -- > > > You received this message because you are subscribed to the Google > Groups "cytoscape-discuss" group. > > > To post to this group, send email to > cytoscape-discuss@googlegroups.com. > > > To unsubscribe from this group, send email to > cytoscape-discuss+unsubscribe@googlegroups.com. > > > For more options, visit this group athttp://
> groups.google.com/group/cytoscape-discuss?hl=en.
Hi Emanuel and Jamal, I had the same problem:
I would like to start Cytoscape remotely without any GUI interface and start CytoscapeRPC automatically to establish a connection with my perl script.
On Tuesday, March 13, 2012 8:04:14 PM UTC, Jamal Theodore wrote:
> Hi Emmanuel,
> Can you share your new CytoscapeRPC version? Starting CytoscapeRPC > without a GUI interface is something I'm interested in too.
> Thanks!
> Jamal
> On Tuesday, February 21, 2012 8:36:31 AM UTC-5, Emanuel wrote:
>> Hi Paul,
>> Many thanks for your reply.
>> Well it’s not exactly what I want, because I would like to start >> Cytoscape remotely without any GUI interface and start CytoscapeRPC >> automatically to establish a connection with my script in python.
>> Though, it’s fine I made the change in CytoscapeRPC source code and >> built it and then added the jar to the plugins folder in Cytoscape. It >> worked :)
>> Thanks.
>> Cheers,
>> On Feb 20, 11:19 pm, Paul Shannon <paul.thurmond.shan...@gmail.com> >> wrote: >> > Hi Emmanuel,
>> > You can setup CyRPC so that it auto-starts on every subsequent >> Cytoscape session. >> > Go to Plugins->CytoscapeRPC->Settings and click "Auto Start"
>> > I hope this helps!
>> > - Paul
>> > On Feb 20, 2012, at 5:02 AM, Emanuel wrote:
>> > > Hi,
>> > > I was wondering if it is possible to activate CytoscapeRPC when >> > > starting Cytoscape through the command line?
>> > > Many thanks.
>> > > Best,
>> > > -- >> > > You received this message because you are subscribed to the Google >> Groups "cytoscape-discuss" group. >> > > To post to this group, send email to cytoscap...@googlegroups.com<javascript:>.
>> > > To unsubscribe from this group, send email to >> cytoscape-disc...@googlegroups.com <javascript:>. >> > > For more options, visit this group athttp://
>> groups.google.com/group/cytoscape-discuss?hl=en.
I just changed CytoscapeRPC source code in order to start it automatically by default, then I generated the jar and put it in Cytoscape plugins folder.
On Friday, September 28, 2012 12:20:01 PM UTC+1, Rossella Rispoli wrote:
> Hi Emanuel and Jamal, > I had the same problem:
> I would like to start Cytoscape remotely without any GUI interface and > start CytoscapeRPC automatically to establish a connection with my perl > script.
> Any suggestion on how can I resolve this problem?
> Many thanks
> Rossella
> On Tuesday, March 13, 2012 8:04:14 PM UTC, Jamal Theodore wrote:
>> Hi Emmanuel,
>> Can you share your new CytoscapeRPC version? Starting CytoscapeRPC >> without a GUI interface is something I'm interested in too.
>> Thanks!
>> Jamal
>> On Tuesday, February 21, 2012 8:36:31 AM UTC-5, Emanuel wrote:
>>> Hi Paul,
>>> Many thanks for your reply.
>>> Well it’s not exactly what I want, because I would like to start >>> Cytoscape remotely without any GUI interface and start CytoscapeRPC >>> automatically to establish a connection with my script in python.
>>> Though, it’s fine I made the change in CytoscapeRPC source code and >>> built it and then added the jar to the plugins folder in Cytoscape. It >>> worked :)
>>> Thanks.
>>> Cheers,
>>> On Feb 20, 11:19 pm, Paul Shannon <paul.thurmond.shan...@gmail.com> >>> wrote: >>> > Hi Emmanuel,
>>> > You can setup CyRPC so that it auto-starts on every subsequent >>> Cytoscape session. >>> > Go to Plugins->CytoscapeRPC->Settings and click "Auto Start"
>>> > I hope this helps!
>>> > - Paul
>>> > On Feb 20, 2012, at 5:02 AM, Emanuel wrote:
>>> > > Hi,
>>> > > I was wondering if it is possible to activate CytoscapeRPC when >>> > > starting Cytoscape through the command line?
>>> > > Many thanks.
>>> > > Best,
>>> > > -- >>> > > You received this message because you are subscribed to the Google >>> Groups "cytoscape-discuss" group. >>> > > To post to this group, send email to cytoscap...@googlegroups.com. >>> > > To unsubscribe from this group, send email to >>> cytoscape-disc...@googlegroups.com. >>> > > For more options, visit this group athttp://
>>> groups.google.com/group/cytoscape-discuss?hl=en.
Hi Emanuel,
many thanks for your replay. I have followed your suggestions: I have set up the variable autoStart in the file SettingsManager.java to "true" instead of to false.(Was that the changing that you did?)
Now if I run the cytoscape with GUI it starts with cytoscapeRPC plugin alredy actived. Aniway if I try to run the perl script to create a cytoscape network (that is present in the folder cytoscaperpc/CytoscapeRPC/tutorial/code/ex_3.pl), without to launch cytoscape with the GUI interface I recive this error:
Can't connect to localhost:9000 (Connection refused).
Have you any suggestions for that? In your process you didn't launch cytoscape before to run the cytoscapeRPC?
On Sunday, September 30, 2012 2:29:48 PM UTC+1, Emanuel wrote:
> Dear Rossella,
> I just changed CytoscapeRPC source code in order to start it automatically > by default, then I generated the jar and put it in Cytoscape plugins > folder.
> Best,
> On Friday, September 28, 2012 12:20:01 PM UTC+1, Rossella Rispoli wrote:
>> Hi Emanuel and Jamal, >> I had the same problem:
>> I would like to start Cytoscape remotely without any GUI interface and >> start CytoscapeRPC automatically to establish a connection with my perl >> script.
>> Any suggestion on how can I resolve this problem?
>> Many thanks
>> Rossella
>> On Tuesday, March 13, 2012 8:04:14 PM UTC, Jamal Theodore wrote:
>>> Hi Emmanuel,
>>> Can you share your new CytoscapeRPC version? Starting CytoscapeRPC >>> without a GUI interface is something I'm interested in too.
>>> Thanks!
>>> Jamal
>>> On Tuesday, February 21, 2012 8:36:31 AM UTC-5, Emanuel wrote:
>>>> Hi Paul,
>>>> Many thanks for your reply.
>>>> Well it’s not exactly what I want, because I would like to start >>>> Cytoscape remotely without any GUI interface and start CytoscapeRPC >>>> automatically to establish a connection with my script in python.
>>>> Though, it’s fine I made the change in CytoscapeRPC source code and >>>> built it and then added the jar to the plugins folder in Cytoscape. It >>>> worked :)
>>>> Thanks.
>>>> Cheers,
>>>> On Feb 20, 11:19 pm, Paul Shannon <paul.thurmond.shan...@gmail.com> >>>> wrote: >>>> > Hi Emmanuel,
>>>> > You can setup CyRPC so that it auto-starts on every subsequent >>>> Cytoscape session. >>>> > Go to Plugins->CytoscapeRPC->Settings and click "Auto Start"
>>>> > I hope this helps!
>>>> > - Paul
>>>> > On Feb 20, 2012, at 5:02 AM, Emanuel wrote:
>>>> > > Hi,
>>>> > > I was wondering if it is possible to activate CytoscapeRPC when >>>> > > starting Cytoscape through the command line?
>>>> > > Many thanks.
>>>> > > Best,
>>>> > > -- >>>> > > You received this message because you are subscribed to the Google >>>> Groups "cytoscape-discuss" group. >>>> > > To post to this group, send email to cytoscap...@googlegroups.com. >>>> > > To unsubscribe from this group, send email to >>>> cytoscape-disc...@googlegroups.com. >>>> > > For more options, visit this group athttp://
>>>> groups.google.com/group/cytoscape-discuss?hl=en.
I'm not sure if I got your question right, but in other to have CytoscapeRPC activated you have to call Cytoscape. The good thing of having CytoscapeRPC automatically activated by default is that you can call Cytoscape from the command line (java -jar cytoscape.jar -p cytoscape/pluginsFolder) and then you can run right-away your perl script.
I was using a python script that I wanted to run in a remote machine without using the GUI. So with CytoscapeRPC automatically activated it was possible to run it through the command line in an automatic fashion way, otherwise it would be impossible.
On Tuesday, October 2, 2012 3:29:19 PM UTC+1, Rossella Rispoli wrote:
> Hi Emanuel,
> many thanks for your replay. > I have followed your suggestions: I have set up the variable autoStart in > the file SettingsManager.java to "true" instead of to false.(Was that the > changing that you did?)
> Now if I run the cytoscape with GUI it starts with cytoscapeRPC plugin > alredy actived. > Aniway if I try to run the perl script to create a cytoscape network (that > is present in the folder cytoscaperpc/CytoscapeRPC/tutorial/code/ex_3.pl), > without to launch cytoscape with the GUI interface I recive this error:
> Can't connect to localhost:9000 (Connection refused).
> Have you any suggestions for that? > In your process you didn't launch cytoscape before to run the cytoscapeRPC?
> Thanks in advances
> Rossella
> On Sunday, September 30, 2012 2:29:48 PM UTC+1, Emanuel wrote:
>> Dear Rossella,
>> I just changed CytoscapeRPC source code in order to start it >> automatically by default, then I generated the jar and put it in Cytoscape >> plugins folder.
>> Best,
>> On Friday, September 28, 2012 12:20:01 PM UTC+1, Rossella Rispoli wrote:
>>> Hi Emanuel and Jamal, >>> I had the same problem:
>>> I would like to start Cytoscape remotely without any GUI interface and >>> start CytoscapeRPC automatically to establish a connection with my perl >>> script.
>>> Any suggestion on how can I resolve this problem?
>>> Many thanks
>>> Rossella
>>> On Tuesday, March 13, 2012 8:04:14 PM UTC, Jamal Theodore wrote:
>>>> Hi Emmanuel,
>>>> Can you share your new CytoscapeRPC version? Starting CytoscapeRPC >>>> without a GUI interface is something I'm interested in too.
>>>> Thanks!
>>>> Jamal
>>>> On Tuesday, February 21, 2012 8:36:31 AM UTC-5, Emanuel wrote:
>>>>> Hi Paul,
>>>>> Many thanks for your reply.
>>>>> Well it’s not exactly what I want, because I would like to start >>>>> Cytoscape remotely without any GUI interface and start CytoscapeRPC >>>>> automatically to establish a connection with my script in python.
>>>>> Though, it’s fine I made the change in CytoscapeRPC source code and >>>>> built it and then added the jar to the plugins folder in Cytoscape. It >>>>> worked :)
>>>>> Thanks.
>>>>> Cheers,
>>>>> On Feb 20, 11:19 pm, Paul Shannon <paul.thurmond.shan...@gmail.com> >>>>> wrote: >>>>> > Hi Emmanuel,
>>>>> > You can setup CyRPC so that it auto-starts on every subsequent >>>>> Cytoscape session. >>>>> > Go to Plugins->CytoscapeRPC->Settings and click "Auto Start"
>>>>> > I hope this helps!
>>>>> > - Paul
>>>>> > On Feb 20, 2012, at 5:02 AM, Emanuel wrote:
>>>>> > > Hi,
>>>>> > > I was wondering if it is possible to activate CytoscapeRPC when >>>>> > > starting Cytoscape through the command line?
>>>>> > > Many thanks.
>>>>> > > Best,
>>>>> > > -- >>>>> > > You received this message because you are subscribed to the Google >>>>> Groups "cytoscape-discuss" group. >>>>> > > To post to this group, send email to cytoscap...@googlegroups.com.
>>>>> > > To unsubscribe from this group, send email to >>>>> cytoscape-disc...@googlegroups.com. >>>>> > > For more options, visit this group athttp://
>>>>> groups.google.com/group/cytoscape-discuss?hl=en.
