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Make Java respect TMPDIR

Status: Open.

#172 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Feb 24, 2022

Passing parameters to qsub

Status: Open.

#171 In UCSF-Costello-Lab/LG3_Pipeline;

· ivan108 opened on Nov 3, 2021

Add built-in support for <code>lg3 run QC1</code>, <code>lg3 run QC2</code>, and <code>lg3 run QC3</code>

Status: Open.

#170 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 19, 2021

LG3 add-on examples assume write permission to ${LG3_HOME}

unreliable-code

Status: Open.

#169 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 12, 2021

REPRODUCIBILITY: lg3 2021-10-11

Status: Open.

#168 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 12, 2021

Add assert_java_1.6() to assert Java is of version 1.6.x

Status: Open.

#166 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 11, 2021

REPRODUCIBILITY: Comparing lg3 2021-10-08 to previous version 2020-05-16

Status: Open.

#161 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 8, 2021

WARN: undefined variables MQRankSum and ReadPosRankSum

Status: Open.

#160 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 8, 2021

PERFORMANCE: ANNOVAR says index file is out of date

Status: Open.

#159 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 8, 2021

RESOURCES: Resource files used

TIPCC-to-C4

Status: Open.

#158 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 8, 2021

·  

Future release (not Next release)

NEWS: Update for important changes

Status: Open.

#156 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 5, 2021

scripts/Align_mem.sh: Why was <code>${SAMTOOLS} index ...</code> dropped?

Status: Open.

#155 In UCSF-Costello-Lab/LG3_Pipeline;

· HenrikBengtsson opened on Oct 5, 2021