ARACNE Manual

[cwyoo]

You can download it and get more information from:

http://en.wikipedia.org/wiki/ARACNE

[meninonas]

Dr. Yoo,

I was having some issues with the installation file so I contacted the individuals from Columbia in order to see if they could assist me.

Nevertheless, I found the following article that I believe could be useful to have.

[cwyoo]

Dr. Yoo,

I was having some issues with the installation file so I contacted the individuals from Columbia in order to see if they could assist me.

Nevertheless, I found the following article that I believe could be useful to have.

I will proceed with or without their assistance. First prepare input data and see whether you need any other files. You might need to search Internet as you move forward. Post your progress here.

[meninonas]

Professor,

It seems that the application isn't meant to be used through Command Prompt as the Protocol itself states "Navigate to the directory where the ARACNE download has been uncompressed". In addition, they actually show a windows through which they do most of the work.

[cwyoo]

Professor,

It seems that the application isn't meant to be used through Command Prompt as the Protocol itself states "Navigate to the directory where the ARACNE download has been uncompressed". In addition, they actually show a windows through which they do most of the work.

Please read the manual that is posted above. It talks about input, output file formats and how to run it in command line.

[meninonas]

Dr. Yoo,

The actual protocol instructs on how to do it besides Command Prompt.

In addition, I'm having downloading JDK 5.0. The Protocol gives the following information:

The GUI is implemented in Java and requires JDK 1.5, which should be downloaded (see EQUIPMENT) by clicking on the link ‘Download JDK 5.0 update 7’ (note that the update number might change if new updates are released after publication of this protocol). The Java installer should set all system variables correctly, including the JAVA_HOME variable, which is required by the program. The version of Java installed on a computer can be determined by typing ‘java version’ at a command prompt.

I've tried downloading it from the following link:

http://www.oracle.com/technetwork/java/ ... 19410.html

Nevertheless, when I try to install the following package jdk-1_5_0_11-linux-i586-rpm.bin, it has errors installing. It gives me the following error:

Code: Select all

Unpacking...
Checksumming...
0
0
Extracting...
UnZipSFX 5.42 of 14 January 2001, by Info-ZIP (Zip-Bugs@lists.wku.edu).
  inflating: jdk-1_5_0_11-linux-i586.rpm 
./jdk-1_5_0_11-linux-i586-rpm.bin: 727: ./jdk-1_5_0_11-linux-i586-rpm.bin: rpm: not found
 
Done.

So I haven't been able to properly install ARACNE.

[cwyoo]

Dr. Yoo,

The actual protocol instructs on how to do it besides Command Prompt.

In addition, I'm having downloading JDK 5.0. The Protocol gives the following information:

The GUI is implemented in Java and requires JDK 1.5, which should be downloaded (see EQUIPMENT) by clicking on the link ‘Download JDK 5.0 update 7’ (note that the update number might change if new updates are released after publication of this protocol). The Java installer should set all system variables correctly, including the JAVA_HOME variable, which is required by the program. The version of Java installed on a computer can be determined by typing ‘java version’ at a command prompt.

I've tried downloading it from the following link:

http://www.oracle.com/technetwork/java/ ... 19410.html

Nevertheless, when I try to install the following package jdk-1_5_0_11-linux-i586-rpm.bin, it has errors installing. It gives me the following error:

Code: Select all

Unpacking...
Checksumming...
0
0
Extracting...
UnZipSFX 5.42 of 14 January 2001, by Info-ZIP (Zip-Bugs@lists.wku.edu).
  inflating: jdk-1_5_0_11-linux-i586.rpm 
./jdk-1_5_0_11-linux-i586-rpm.bin: 727: ./jdk-1_5_0_11-linux-i586-rpm.bin: rpm: not found
 
Done.

So I haven't been able to properly install ARACNE.

Seems we'll need to look further in this. Also, please work on commad line option in parallel.

[meninonas]

Dr. Yoo,

The way that the instruction manual is written, it seems that this installation is required regardless of Command Prompt.

[cwyoo]

Dr. Yoo,

The way that the instruction manual is written, it seems that this installation is required regardless of Command Prompt.

The command line program is a stand alone program (no installation needed). You can run it by reading the manual that I posted on Thu Mar 05, 2015 2:27 pm in this forum.

[meninonas]

Dr. Yoo,

I've been able to get the correct command for inputting the data into ARACNE. Nevertheless, I get the following error:

Code: Select all

 
[PARA] InputFile:     /luis/Downloads/MasterFile.txt
[PARA] Output File:
[PARA] Algorithm:     fixed_bandwidth 
[PARA] Kernel width:  determined by program
[PARA] MI P-value:    1
[PARA] DPI Tolerance: 1
Bad File
Problem with reading the file.


I've been playing around with the file setup to make sure it matches the one with the manual you provided. I'll continue on Monday.