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update for SD4H deployment #17

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Merged
davidlougheed merged 8 commits into from
Apr 30, 2025
Merged

update for SD4H deployment #17

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db0b17f
docs: readme link to application note [no ci]
davidlougheed Apr 29, 2025
173de3d
chore(server): update lockfile deps
davidlougheed Apr 29, 2025
4a35229
chore(client): update lockfile
davidlougheed Apr 29, 2025
8617992
chore: bump version to 1.0.1
davidlougheed Apr 29, 2025
128a972
chore(client): update lockfile
davidlougheed Apr 29, 2025
f53ed1a
update compose file for SD4H deployment
davidlougheed Apr 29, 2025
11bd81e
chore: update base images
davidlougheed Apr 29, 2025
2b7ec63
fix(client): build issue
davidlougheed Apr 30, 2025
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3,788 changes: 2,080 additions & 1,708 deletions client/package-lock.json
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3 changes: 2 additions & 1 deletion client/package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "flu-infection-client",
"version": "1.0.0",
"version": "1.0.1",
"private": true,
"dependencies": {
"@redux-devtools/extension": "^3.2.6",
Expand Down Expand Up @@ -43,6 +43,7 @@
],
"devDependencies": {
"@babel/plugin-proposal-private-property-in-object": "^7.21.11",
"@babel/plugin-syntax-dynamic-import": "^7.8.3",
"@babel/preset-env": "^7.23.6",
"@babel/preset-react": "^7.23.3",
"babel-loader": "^9.1.3",
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34 changes: 17 additions & 17 deletions epivar-prod/docker-compose.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,23 +39,23 @@ services:
- ./node1/about.md:/app/data/about.md
- ./node1/config.js:/app/config.js:ro
# genotypes: VCF + index file
- /flu-infection-data/node1/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz:/app/data/genotypes.vcf.gz:ro
- /flu-infection-data/node1/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro
- /data/flu-infection-data/node1/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz:/app/data/genotypes.vcf.gz:ro
- /data/flu-infection-data/node1/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro
# peaks files
- /flu-infection-data/node1/matrices:/app/input-files/matrices:ro
- /flu-infection-data/node1/qtls:/app/input-files/qtls:ro
- /data/flu-infection-data/node1/matrices:/app/input-files/matrices:ro
- /data/flu-infection-data/node1/qtls:/app/input-files/qtls:ro
# tracks:
# - metadata JSON file,
- ./node1/metadata.json:/app/data/metadata.json:ro
# - sample bigWigs,
- /flu-infection-data/ATACseq:/tracks/ATACseq:ro
- /flu-infection-data/H3K27ac:/tracks/H3K27ac:ro
- /flu-infection-data/H3K27me3:/tracks/H3K27me3:ro
- /flu-infection-data/H3K4me1:/tracks/H3K4me1:ro
- /flu-infection-data/H3K4me3:/tracks/H3K4me3:ro
- /flu-infection-data/RNAseq:/tracks/RNAseq:ro
- /data/flu-infection-data/ATACseq:/tracks/ATACseq:ro
- /data/flu-infection-data/H3K27ac:/tracks/H3K27ac:ro
- /data/flu-infection-data/H3K27me3:/tracks/H3K27me3:ro
- /data/flu-infection-data/H3K4me1:/tracks/H3K4me1:ro
- /data/flu-infection-data/H3K4me3:/tracks/H3K4me3:ro
- /data/flu-infection-data/RNAseq:/tracks/RNAseq:ro
# - writeable volume for on-the-fly merged tracks,
- /flu-infection-data/node1/mergedTracks:/mergedTracks
- /data/flu-infection-data/node1/mergedTracks:/mergedTracks
# - other static tracks for showing in the UCSC browser.
- ./node1/ucsc.other-tracks.txt:/app/data/ucsc.other-tracks.txt:ro

Expand Down Expand Up @@ -100,18 +100,18 @@ services:
- ./node2/about.md:/app/data/about.md
- ./node2/config.js:/app/config.js:ro
# genotypes: VCF + index file
- /flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.GRCh38.vcf.gz:/app/data/genotypes.vcf.gz:ro
- /flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.GRCh38.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro
- /data/flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.GRCh38.vcf.gz:/app/data/genotypes.vcf.gz:ro
- /data/flu-infection-data/node2/allSamples.hc.vqsr.mil.snpId.snpeff.dbnsfp.GRCh38.vcf.gz.tbi:/app/data/genotypes.vcf.gz.tbi:ro
# peaks files
- /flu-infection-data/node2/matrices:/app/input-files/matrices:ro
- /flu-infection-data/node2/qtls:/app/input-files/qtls:ro
- /data/flu-infection-data/node2/matrices:/app/input-files/matrices:ro
- /data/flu-infection-data/node2/qtls:/app/input-files/qtls:ro
# tracks:
# - metadata JSON file,
- ./node2/metadata.json:/app/data/metadata.json:ro
# - sample bigWigs,
- /flu-infection-data/node2/tracks:/tracks:ro
- /data/flu-infection-data/node2/tracks:/tracks:ro
# - writeable volume for on-the-fly merged tracks,
- /flu-infection-data/node2/mergedTracks:/mergedTracks
- /data/flu-infection-data/node2/mergedTracks:/mergedTracks
# - other static tracks for showing in the UCSC browser.
# *** NONE FOR NODE 2 ***

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