Software Deprecation: Java#

30 September 2020

Please be advised of upcoming changes to the Java software modules on the system.

On Thursday, the 15th of October, 2020, we will be removing these two java software modules:

  • java/1.7.0_67

  • java/1.8.0_77

This change is necessary as critical security vulnerabilities are present in these two versions of Java.

In their place, please use:

  • java/openjdk-1.8.0_242

  • java/openjdk-1.14.02

This change requires updating the java version that underpins the following 26 specific versions of software modules:

Module Name

Version/s

beagle

2.1.2 3.1.2

fastqc

0.11.7

gatk

3.4 3.7 4.0.1.1 4.0.11.0 4.1.2.0

gem

3.3

juicer

1.6.2

mauve

20150213

maven

3.3.9

nighres

1.1.0b1

nilearn

0.6.2

picard

2.9.2 2.19.0

R

3.5.1 3.5.2-openblas 3.5.3-mkl 3.6.0-mkl 3.6.2-mkl 4.0.0-openblas

snpeff

4.3t

swig

3.0.12 4.0.1

xnat-desktop

1.0.40

Ahead of the removal of these older java modules, on October 8, 2020 (Thursday), these modules will be updated to use java/openjdk-1.8.0_242. As the difference of this java is the patch number (from the old _77 to the updated _242), we do not expect this to affect the correct operation of these modules. We have conducted simple tests to ensure that the commands for each of these modules work under the patched java.

Please advise us if there are any issues: help@massive.org.au