This is a test version of Biostars. For the public version, visit https://www.biostars.org.
can't run Aracne -- Java error

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:

$ 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!

aracne rna-seq network

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

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

/path/to/aracne2.macosx

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

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

1 answer

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.

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

Log in to answer this question.