CLEANUP: Use same JAVA everywhere

[HenrikBengtsson]

$ grep -iE "^java" -r --include="*.sh"
scripts/Merge_QC.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java
scripts/Recal_step.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java
scripts/FixReadGroups.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java
scripts/Recal.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java
scripts/Mutect2_TvsN.sh:java -version
scripts/Recal_pass2.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java
scripts/MutDet.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java
scripts/Align_mem.sh:JAVA=java
scripts/Merge.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java
scripts/Align_fastq.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java
scripts/Germline.sh:JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java

[HenrikBengtsson]

Meeting notes from 2021-10-01:

scripts/Align_mem.sh:JAVA=java

These are not used in the default pipeline, because we still use the old BWA aligner. Thus, if we change, our redundancy checks won't test it anyway.

Decision:

• [x] Update to JAVA=${LG3_HOME}/tools/java/jre1.6.0_27/bin/java to make sure we're all running the same version and to align with the rest of the code.
• [x] Document this change in the NEWS file.

Hopefully it won't make a difference; we just have to cross our fingers that it wont

[HenrikBengtsson]

This was fixed in 2021-05-26, cf. https://github.com/UCSF-Costello-Lab/LG3_Pipeline/issues/139