From 0ef593f01321ee7d782cd09d37b4924874c2497b Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 24 Sep 2024 12:54:07 -0700 Subject: [PATCH 1/2] Allow more memory for CacheAlignerIndexesTask --- .../primeseq/pipeline/SequenceJobResourceAllocator.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java b/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java index 685c97047..382fe9551 100644 --- a/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java +++ b/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java @@ -168,8 +168,8 @@ public Integer getMaxRequestMemory(PipelineJob job) // NOTE: STAR in particular needs more memory if (isCacheAlignerIndexesTask(job)) { - job.getLogger().debug("setting memory to 24"); - return 24; + job.getLogger().debug("setting memory to 36"); + return 36; } if (isLuceneIndexJob(job)) From 93e150a0a2475493337c092fa0eaaf7647732de9 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 25 Sep 2024 10:08:56 -0700 Subject: [PATCH 2/2] Augment kinship calculation to check modification date and only run as-needed (#172) --- PMR/resources/queries/study/pedigree.sql | 3 ++- mcc/resources/queries/study/pedigree.sql | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/PMR/resources/queries/study/pedigree.sql b/PMR/resources/queries/study/pedigree.sql index c18ce19e6..404b359a4 100644 --- a/PMR/resources/queries/study/pedigree.sql +++ b/PMR/resources/queries/study/pedigree.sql @@ -23,7 +23,8 @@ AS status, d.id.demographics.calculated_status as status_code, d.id.demographics.species, '' as Display, -'Demographics' as source +'Demographics' as source, +d.modified FROM study.demographicsParents d WHERE d.numParents > 0 and d.id.demographics.species IS NOT NULL \ No newline at end of file diff --git a/mcc/resources/queries/study/pedigree.sql b/mcc/resources/queries/study/pedigree.sql index c18ce19e6..404b359a4 100644 --- a/mcc/resources/queries/study/pedigree.sql +++ b/mcc/resources/queries/study/pedigree.sql @@ -23,7 +23,8 @@ AS status, d.id.demographics.calculated_status as status_code, d.id.demographics.species, '' as Display, -'Demographics' as source +'Demographics' as source, +d.modified FROM study.demographicsParents d WHERE d.numParents > 0 and d.id.demographics.species IS NOT NULL \ No newline at end of file