A question on how to close dchip window from command line

[Cheng Li]

Hi Aiguo,

 

> Can I somehow put an exit or termination signal in the module?

 

This is a good suggestion. Please try this 1/22 version: http://biosun1.harvard.edu/~cli/dchip.exe

 

To let dChip shut down, put the string “EXIT_DCHIP” in the comment of the last automation step. You can do this through “Tools/Automate” menu, or edit the *.auto.xml file in a text editor:

 

<step>

<type>Clustering/Correlation Matrix</type>

<name/>

<selected>Yes</selected>

<comments>EXIT_DCHIP</comments>

</step>

 

Cheng

 

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From: Li, Aiguo (NIH/NCI) [E] [mailto:li...@mail.nih.gov]
Sent: Thursday, January 22, 2009 4:58 PM
To: Cheng Li
Subject: RE: A question on how to close dchip window from command line

 

Dear Dr. Li,

 

I tried system(“taskkill /f /im dchip.exe”) and it works if I already have a dchip window open.  However, if I run system(“dchip”); system(“taskkill /f /im dchip.exe”) consequently, it does not work.  It seems to me that the system will hang in there after the normalization is done and it does not proceed to the completion mode. However, the “taskkill /f /im dchip.exe” works after the running is done.  In the automatic module, I have three steps included: 1) open group, 2) normalization, 3) expression output.  Can I somehow put an exit or termination signal in the module?

 

Thanks for your help!

 

Aiguo

 

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From: Cheng Li [mailto:c...@hsph.harvard.edu]
Sent: Wednesday, January 21, 2009 12:26 PM
To: Li, Aiguo (NIH/NCI) [E]
Subject: RE: A question on how to close dchip window from command line

 

How about using “taskkill /IM dchip.exe” in system()?

 

Cheng

 

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From: Li, Aiguo (NIH/NCI) [E] [mailto:li...@mail.nih.gov]
Sent: Wednesday, January 21, 2009 9:09 AM
To: Cheng Li
Subject: RE: A question on how to close dchip window from command line

 

Morning, Dr. Li.

 

I tried the following commands and none of them worked.

system(“tskill dchip”);

system(“tskill dchip.ext”);

system(“tskill pid#”);

 

However, system(“dchip”) is starting the normalization process.

 

Thanks and have a nice day!

 

Aiguo

 

 

 

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From: Cheng Li [mailto:c...@hsph.harvard.edu]
Sent: Friday, January 16, 2009 7:25 PM
To: Li, Aiguo (NIH/NCI) [E]
Subject: RE: A question on how to close dchip window from command line

 

Aiguo,

 

Does system("tskill dchip") work?

 

Cheng

 

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From: Li, Aiguo (NIH/NCI) [E] [mailto:li...@mail.nih.gov]
Sent: Friday, January 16, 2009 11:25 AM
To: Cheng Li
Subject: A question on how to close dchip window from command line

 

Dear Dr. Li,

 

I really appreciate your effort for providing me the new build that allow me to specify baseline array using automate module.  I now was able to run dchip from perl script to normalize my upcoming new arrays using the following command in perl.  

 

Ø      system(dchip);

This line will start the dchip normalization process including opengroup, normalization and export expression in my case and same the output files in a defined directory.  In the mean while it also open dchip window.  Since the normalization process in my case is a continuous process over time, I could not allow many dchip windows open on my machine.  Therefore I need somehow to close dchip window after each normalization.  In DOS mode I was able to close the dchip window using “tskill” command, but it does not work in perl script.   Could you please offer me some suggestions on how to handle this issue?

 

Thanks in advance and have a happy Spring Festival!

 

Aiguo Li

[Li, Aiguo (NIH/NCI) [E]]

Dr. Cheng Li,

 

I tried to edit the .auto file following your instruction, but it seems not helping because the dchip is still idling there after doing the normalization.  The worst is that it does not proceed to execute any line of codes following the system(“dchip”).  I have attached several snapshots for helping you to understand what I am talking about.  In this sceneries, I definitely need to have a way to terminate the process of the automate module because I need to run the perl code after normalization to format the data for our prediction tool.  I really appreciate of any further suggestions….

 

Thank you so much!

 

Aiguo Li

[Cheng Li]

Hi Aiguo,

 

Could you attach or copy or your *.auto.xml file? Are you using a dChip version 1/22 or later?

 

Cheng

 

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[Li, Aiguo (NIH/NCI) [E]]

Dear Dr. Li,

 

Per your request, I am attaching to you my .auto file.  As you noticed, the last line before the step is exit_dchip.  One more thing I noticed is that the dchip opened by system(“dchip”) is a version created on Jan. 8 when checking the Help\About dchip although I used the Jan. 27 version of dchip to generate the automate module and have it in my C:\dchip\wk folder.  My question to you is where the dchip application to get the dchip file when I ran system(“dchip”) by default?  Is there a way I could assign the folder for system(“dchip”) to find the right file.  By the way, I do have a network drive where we store all the previous dchip files downloaded from your site.

 

Thanks for your help!

 

Aiguo

 

[Cheng Li]

Aiguo,

 

Make sure you use uppercase “EXIT_DCHIP” in the automation file.

 

To use specific dChip versions, may be you can try to add directory to system()? e.g. system(“c:\dchip\dchip.exe”).