Java versions: Difference between Gloria and Helena

[hengnck]

Hi All,
I've just upgraded (and a happy donator too!) from Gloria to Helena. My query is regarding the differences between the implementation of Java in Helena compared to Gloria. I have a 32-bit bioinformatics (DNA analysis) software package that runs beautifully on Gloria but fails in Helena - the 64-bit version of the package generates errors in Helena x64. Other bits of info: The package installs a folder which contains JRE1.5.0_07 and presumably calls the subroutines from within that folder. I would be most grateful if any of you gurus could help me out here.
Also - if anyone can explain the differences between sh and bash as when I change the execution scripts to bash (from sh), the software works! Yes, I'm a newbie at Linux (and command line), and yes, the bioinformatics package scripts appear to be poorly written or very inflexible. The package was supposedly written for Red Hat Enterprise Linux (which sucks) and its derivatives (e.g., CentOS).
Thanks in advance and Cheers!!!

[pompom]

Welcome to Linux Mint!

There are no differences between Java in Helena and Gloria. You will find "hard to diagnose" differences though between virtual machine vendor versions, so your best bet is sun-java6-jdk. When it comes to java you need to redirect to a file just to see the choices. When you upgrade from Gloria to Helena, some packages need to be reinstalled. Did you save your apt profile before upgrade?

Code: Select all

java -version
sudo apt-cache search java >> out_java.txt
echo "Runtime environment options:" >> out_java.txt
sudo apt-cache search jre >> out_java.txt
cat out_java.txt | less

The main difference between sh and bash is that sh is on steroids. You can inspect them here. When writing/executing scripts change the first line to

Code: Select all

#!/bin/bash

Cheers,

pompom

[hengnck]

Thanks for the info about sun-java and bash, pompom.

I did not upgrade to Helena from Gloria - just backed up all my data and performed a clean install. I'm more convinced that the software I'm using is just really poorly-written and I may have to consider sticking with Gloria on that dedicated workstation. All other bioinformatics packages work fine on both Mint versions. There are several other available (and apparently more user-friendly) alternatives to this particular piece of software but at the cost of $300, I expect it to work on all Linux flavours!

Cheers again!