can't run Aracne -- Java error

Question

[rioualen]

Hello, I'm trying to run Aracne in order to generate network data from expression data. I can't seem to run the program, despite trying different versions:

• I downloaded the MacOS file from there http://califano.c2b2.columbia.edu/aracne but I don't know how to use the .macosx file

• I downloaded the jar file from the same website, but it seems it does not work with the option --tfs

• I downloaded the sourceforge version https://sourceforge.net/p/aracne-ap/wiki/Home/?version=9 but it throws a Java error that I did not find how to manage (even when running the example data and commands provided):

$ java -Xmx5G -jar Aracne.jar -e matrix.txt  -o outputFolder --tfs tfs.txt --pvalue 1E-8 --seed 1 -–calculateThreshold
Exception in thread "main" java.lang.NoClassDefFoundError: jargs/gnu/CmdLineParser$OptionException
  at java.base/java.lang.Class.forName0(Native Method)
  at java.base/java.lang.Class.forName(Class.java:398)
  at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:56)
Caused by: java.lang.ClassNotFoundException: jargs.gnu.CmdLineParser$OptionException
  at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:471)
  at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:588)
  at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
  ... 3 more
  

I'm on macOS Mojave and openjdk 11.0.2

Any help will be greatly appreciated!

[Ram]

The macOS download seems to be an executable. Try the following steps:

1. chmod u+x <macos_download_file>.macosx
2. bash <macos_download_file>.macosx

macOS might restrict the script because it is from an "unknown source" If it does that, follow these steps: https://www.macworld.co.uk/how-to/mac-software/mac-app-unidentified-developer-3669596/ (you should see the "Open Anyway" option)

[rioualen]

The bash command gets me a aracne2.macosx: aracne2.macosx: cannot execute binary file error. And when trying to open outside of the terminal macos does not know which application to execute it with

[Ram]

Ah, it's not an installer. Try running it directly from the shell.

/path/to/aracne2.macosx

[rioualen]

I get that: Cannot find file "usage.txt"! Please make sure it is in the current working directory.

[Federico Giorgi]

Aracne-AP is written for Java8, which back then (2015) was the standard!

Answer 1

[rioualen]

I tried running Aracne (sourceforge version) on my old laptop and it worked just fine (Ubuntu 16.04 + openjdk 1.8.92).

So in my macbook I created a conda environment, installed an old Java version in there (opendjdk 8.0.192) and Aracne is running fine.

[Ram]

Thank you for following up. Please accept your answer so the question is marked as solved.