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Merge discvr-21.7 to develop
2 parents 02149ec + ab00998 commit bafa517

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+1894
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‎SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java‎

Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -394,6 +394,20 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa
394394
toolParams.add("--genomicsdb-shared-posixfs-optimizations");
395395
}
396396

397+
Integer maxRam = SequencePipelineService.get().getMaxRam();
398+
int nativeMemoryBuffer = ctx.getParams().optInt("variantCalling.GenotypeGVCFs.nativeMemoryBuffer", 0);
399+
if (maxRam != null && nativeMemoryBuffer > 0)
400+
{
401+
ctx.getLogger().info("Adjusting RAM based on memory buffer (" + nativeMemoryBuffer + ")");
402+
maxRam = maxRam - nativeMemoryBuffer;
403+
404+
if (maxRam < 1)
405+
{
406+
throw new PipelineJobException("After adjusting for nativeMemoryBuffer, maxRam is less than 1: " + maxRam);
407+
}
408+
wrapper.setMaxRamOverride(maxRam);
409+
}
410+
397411
wrapper.execute(genome.getWorkingFastaFile(), outputVcf, toolParams, inputVcf);
398412
try
399413
{

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetCreationTask.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -607,3 +607,4 @@ private SequencePipelineSettings getSettings()
607607
return _settings;
608608
}
609609
}
610+

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -345,6 +345,12 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i
345345
if (vcList.isEmpty())
346346
{
347347
job.getLogger().error("Cannot find matching NT SNP: " + aa.toString());
348+
if (aa.containsKey("refContext") && aa.getString("refContext").length() > 4)
349+
{
350+
// Skip complex indels with just a logged error, but let the job finish
351+
continue;
352+
}
353+
348354
throw new PipelineJobException("Expected variant for AA position: " + aaName + " " + pos);
349355
}
350356

‎cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -725,7 +725,11 @@ protected List<String> execute(String command)
725725
String output = IOUtils.toString(p.getInputStream(), StringUtilsLabKey.DEFAULT_CHARSET);
726726
String errorOutput = IOUtils.toString(p.getErrorStream(), StringUtilsLabKey.DEFAULT_CHARSET);
727727

728-
p.waitFor();
728+
int exitCode = p.waitFor();
729+
if (exitCode != 0)
730+
{
731+
_log.error("Non-zero exit from command: " + command);
732+
}
729733

730734
if (errorOutput != null)
731735
{

‎cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -88,6 +88,10 @@ protected List<String> submitJobToCluster(ClusterJob j, PipelineJob job) throws
8888
}
8989
}
9090
}
91+
else
92+
{
93+
_log.info("No output returned after slurm command: " + command);
94+
}
9195

9296
if (j.getClusterId() == null)
9397
{

‎jbrowse/package-lock.json‎

Lines changed: 342 additions & 266 deletions
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‎jbrowse/package.json‎

Lines changed: 8 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -6,19 +6,23 @@
66
"setup": "npm ci",
77
"build": "npm run build-dev",
88
"start": "cross-env NODE_ENV=development LK_MODULE_CONTAINER=DiscvrLabKeyModules LK_MODULE=jbrowse webpack-dev-server --config config/watch.config.js",
9-
"build-dev": "npm run clean && cross-env NODE_ENV=development LK_MODULE_CONTAINER=DiscvrLabKeyModules LK_MODULE=jbrowse webpack --config config/dev.config.js --progress --profile && npm run jb-pkg",
9+
"build-no-pkg": "npm run clean && cross-env NODE_ENV=development LK_MODULE_CONTAINER=DiscvrLabKeyModules LK_MODULE=jbrowse webpack --config config/dev.config.js --progress --profile",
10+
"build-dev": "npm run build-no-pkg && npm run jb-pkg",
1011
"build-prod": "npm run clean && cross-env NODE_ENV=production PROD_SOURCE_MAP=source-map LK_MODULE_CONTAINER=DiscvrLabKeyModules LK_MODULE=jbrowse webpack --config config/prod.config.js --progress --profile && npm run jb-pkg",
1112
"clean": "rimraf resources/web/jbrowse/gen && rimraf resources/views/gen && rimraf resources/views/browser*",
1213
"test": "cross-env NODE_ENV=test jest",
1314
"jb-pkg": "pkg ./node_modules/@jbrowse/cli --out-path ./resources/external/jb-cli"
1415
},
1516
"dependencies": {
1617
"@jbrowse/cli": "^1.4.4",
17-
"@jbrowse/react-linear-genome-view": "^1.4.4",
18+
"@jbrowse/react-linear-genome-view": "^1.5.0",
1819
"@labkey/components": "2.67.1",
1920
"assert": "^2.0.0",
2021
"browserify-zlib": "^0.2.0",
2122
"buffer": "^6.0.3",
23+
"mobx": "^5.0.0",
24+
"mobx-react": "^6.0.0",
25+
"mobx-state-tree": "3.14.1",
2226
"node-polyfill-webpack-plugin": "1.1.0",
2327
"path-browserify": "^1.0.1",
2428
"pkg": "^5.3.2",
@@ -30,7 +34,6 @@
3034
"vm-browserify": "^1.1.2"
3135
},
3236
"devDependencies": {
33-
"rimraf": "~3.0.2",
3437
"@labkey/build": "^4.0.1",
3538
"@types/enzyme": "^3.10.9",
3639
"@types/jest": "^27.0.1",
@@ -40,9 +43,10 @@
4043
"enzyme-adapter-react-16": "^1.15.6",
4144
"enzyme-to-json": "^3.6.2",
4245
"jest": "^27.2.0",
43-
"jest-teamcity-reporter": "^0.9.0",
4446
"jest-cli": "^27.2.0",
47+
"jest-teamcity-reporter": "^0.9.0",
4548
"react-test-renderer": "^17.0.2",
49+
"rimraf": "~3.0.2",
4650
"ts-jest": "^27.0.5"
4751
},
4852
"browser": {

‎jbrowse/resources/external/mGAPFilteredSession.json‎

Lines changed: 120 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,120 @@
1+
{
2+
"configuration": {},
3+
"assembly": {
4+
"name": "hg38",
5+
"aliases": [
6+
"GRCh38"
7+
],
8+
"sequence": {
9+
"type": "ReferenceSequenceTrack",
10+
"trackId": "P6R5xbRqRr",
11+
"adapter": {
12+
"type": "BgzipFastaAdapter",
13+
"fastaLocation": {
14+
"uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
15+
},
16+
"faiLocation": {
17+
"uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
18+
},
19+
"gziLocation": {
20+
"uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
21+
}
22+
}
23+
},
24+
"refNameAliases": {
25+
"adapter": {
26+
"type": "RefNameAliasAdapter",
27+
"location": {
28+
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
29+
}
30+
}
31+
}
32+
},
33+
"location": "1:1..248,956,422",
34+
"tracks": [
35+
{
36+
"type": "ExtendedVariantTrack",
37+
"trackId": "mgap_hg38",
38+
"name": "mgap",
39+
"assemblyNames": [
40+
"hg38"
41+
],
42+
"category": [
43+
"Annotation"
44+
],
45+
"adapter": {
46+
"type": "ExtendedVariantAdapter",
47+
"vcfGzLocation": {
48+
"uri": "<%=contextPath%>/jbrowse/mgap/mGap.v2.1.subset.vcf.gz"
49+
},
50+
"index": {
51+
"location": {
52+
"uri": "<%=contextPath%>/jbrowse/mgap/mGap.v2.1.subset.vcf.gz.tbi"
53+
}
54+
},
55+
"filters": [
56+
"AF:lt:0.001",
57+
"AC:lt:6",
58+
"IMPACT:eq:'MODERATE'"
59+
]
60+
},
61+
"displays": [
62+
{
63+
"type": "ExtendedVariantDisplay",
64+
"displayId": "mgap_hg38-ExtendedVariantDisplay",
65+
"renderer": {
66+
"type": "ExtendedVariantRenderer",
67+
}
68+
}
69+
],
70+
"metadata": {
71+
"extendedVariantDisplayConfig": [
72+
{
73+
"name": "AC, AF",
74+
"properties": [
75+
"AC",
76+
"AF",
77+
"IMPACT"
78+
]
79+
},
80+
{
81+
"name": "LF, MAF",
82+
"properties": [
83+
"LF",
84+
"MAF"
85+
]
86+
},
87+
{
88+
"name": "ERBSEG_NM, ERBSEG_CT, SX",
89+
"properties": [
90+
"ERBSEG_NM",
91+
"ERBSEG_CT",
92+
"SX"
93+
]
94+
}
95+
],
96+
"message": "\n\nAut molestiae temporibus nesciunt. Sed repellendus incidunt et. Inventore vitae tempora consequuntur maiores veritatis blanditiis voluptates explicabo.\n\nSimilique aliquid vel occaecati labore corporis adipisci provident voluptas."
97+
}
98+
}
99+
],
100+
"connections": [],
101+
"defaultSession": {
102+
"name": "Test Session",
103+
"view": {
104+
"id": "linearGenomeView",
105+
"type": "LinearGenomeView",
106+
"tracks": [
107+
{
108+
"type": "ExtendedVariantTrack",
109+
"configuration": "mgap_hg38",
110+
"displays": [
111+
{
112+
"type": "ExtendedVariantDisplay",
113+
"configuration": "mgap_hg38-ExtendedVariantDisplay"
114+
}
115+
]
116+
}
117+
]
118+
}
119+
}
120+
}

‎jbrowse/resources/external/mGAPInvalidFilteredSession.json‎

Lines changed: 124 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,124 @@
1+
{
2+
"configuration": {},
3+
"assembly": {
4+
"name": "hg38",
5+
"aliases": [
6+
"GRCh38"
7+
],
8+
"sequence": {
9+
"type": "ReferenceSequenceTrack",
10+
"trackId": "P6R5xbRqRr",
11+
"adapter": {
12+
"type": "BgzipFastaAdapter",
13+
"fastaLocation": {
14+
"uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
15+
},
16+
"faiLocation": {
17+
"uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
18+
},
19+
"gziLocation": {
20+
"uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
21+
}
22+
}
23+
},
24+
"refNameAliases": {
25+
"adapter": {
26+
"type": "RefNameAliasAdapter",
27+
"location": {
28+
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
29+
}
30+
}
31+
}
32+
},
33+
"location": "1:1..248,956,422",
34+
"tracks": [
35+
{
36+
"type": "ExtendedVariantTrack",
37+
"trackId": "mgap_hg38",
38+
"name": "mgap",
39+
"assemblyNames": [
40+
"hg38"
41+
],
42+
"category": [
43+
"Annotation"
44+
],
45+
"adapter": {
46+
"type": "ExtendedVariantAdapter",
47+
"vcfGzLocation": {
48+
"uri": "<%=contextPath%>/jbrowse/mgap/mGap.v2.1.subset.vcf.gz"
49+
},
50+
"index": {
51+
"location": {
52+
"uri": "<%=contextPath%>/jbrowse/mgap/mGap.v2.1.subset.vcf.gz.tbi"
53+
}
54+
},
55+
"filters": [
56+
"INVALID:lt:0.001",
57+
"AC:INVALID:6",
58+
"AC:lt:HIGH",
59+
"IMPACT:eq:INVALID",
60+
"IMPACT:gt:'LOW'",
61+
"IMPACT:eq:LOW",
62+
"IMPACT:eq:'HIGH'"
63+
]
64+
},
65+
"displays": [
66+
{
67+
"type": "ExtendedVariantDisplay",
68+
"displayId": "mgap_hg38-ExtendedVariantDisplay",
69+
"renderer": {
70+
"type": "ExtendedVariantRenderer",
71+
}
72+
}
73+
],
74+
"metadata": {
75+
"extendedVariantDisplayConfig": [
76+
{
77+
"name": "AC, AF",
78+
"properties": [
79+
"AC",
80+
"AF",
81+
"IMPACT"
82+
]
83+
},
84+
{
85+
"name": "LF, MAF",
86+
"properties": [
87+
"LF",
88+
"MAF"
89+
]
90+
},
91+
{
92+
"name": "ERBSEG_NM, ERBSEG_CT, SX",
93+
"properties": [
94+
"ERBSEG_NM",
95+
"ERBSEG_CT",
96+
"SX"
97+
]
98+
}
99+
],
100+
"message": "\n\nAut molestiae temporibus nesciunt. Sed repellendus incidunt et. Inventore vitae tempora consequuntur maiores veritatis blanditiis voluptates explicabo.\n\nSimilique aliquid vel occaecati labore corporis adipisci provident voluptas."
101+
}
102+
}
103+
],
104+
"connections": [],
105+
"defaultSession": {
106+
"name": "Test Session",
107+
"view": {
108+
"id": "linearGenomeView",
109+
"type": "LinearGenomeView",
110+
"tracks": [
111+
{
112+
"type": "ExtendedVariantTrack",
113+
"configuration": "mgap_hg38",
114+
"displays": [
115+
{
116+
"type": "ExtendedVariantDisplay",
117+
"configuration": "mgap_hg38-ExtendedVariantDisplay"
118+
}
119+
]
120+
}
121+
]
122+
}
123+
}
124+
}

‎jbrowse/resources/external/mGAPSession.json‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@
3030
}
3131
}
3232
},
33-
"location": "1:1..248,956,422",
33+
"location": "1:116,089,906..117,411,914",
3434
"tracks": [
3535
{
3636
"type": "ExtendedVariantTrack",
@@ -57,8 +57,9 @@
5757
{
5858
"type": "ExtendedVariantDisplay",
5959
"displayId": "mgap_hg38-ExtendedVariantDisplay",
60+
"maxDisplayedBpPerPx": 2000,
6061
"renderer": {
61-
"type": "ExtendedVariantRenderer",
62+
"type": "ExtendedVariantRenderer"
6263
}
6364
}
6465
],

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