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Initial Framework Setup #2

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merged 2 commits into from
Sep 4, 2024
Merged

Initial Framework Setup #2

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264b6d1
first draft
Taepper Sep 3, 2024
8ee2d62
Some docker compose fixes
Taepper Sep 3, 2024
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50 changes: 50 additions & 0 deletions docker-compose.yml
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Original file line number Diff line number Diff line change
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services:
lapisOpen:
image: ghcr.io/genspectrum/lapis:${LAPIS_TAG}
ports:
- "8080:8080"
command: --silo.url=http://silo:8081
volumes:
- type: bind
source: ${TESTSET_DATA_FOLDER}/database_config.yaml
target: /workspace/database_config.yaml
read_only: true
- type: bind
source: ${TESTSET_DATA_FOLDER}/reference_genomes.json
target: /workspace/reference_genomes.json
read_only: true

silo:
image: ghcr.io/genspectrum/lapis-silo:${SILO_TAG}
ports:
- "8081:8081"
command: --api
volumes:
- type: bind
source: ${TESTSET_OUTPUT_FOLDER}/
target: /data
read_only: true
depends_on:
siloPreprocessing:
condition: service_completed_successfully

siloPreprocessing:
image: ghcr.io/genspectrum/lapis-silo:${SILO_TAG}
command: --preprocessing
volumes:
- type: bind
source: ${TESTSET_OUTPUT_FOLDER}/
target: /preprocessing/output
read_only: false
- type: bind
source: ${TESTSET_DATA_FOLDER}/
target: /preprocessing/input
read_only: false
- type: bind
source: ${TESTSET_DATA_FOLDER}/preprocessingConfig.yaml
target: /app/preprocessing_config.yaml
read_only: true
- type: bind
source: ${TESTSET_DATA_FOLDER}/database_config.yaml
target: /app/database_config.yaml
read_only: true
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