diff --git a/DemoStack/.env b/DemoStack/.env index 2e092a4..46eeb86 100644 --- a/DemoStack/.env +++ b/DemoStack/.env @@ -74,7 +74,7 @@ MinioBrowser=http://localhost:9000 # MinioServerApi=http://127.0.0.1:9000 TesAPIUrl=http://funnel:8000/v1/tasks # Where TESK or Funnel API is hosted: FunnelMinioUser=miniofunnel FunnelMinioPass=miniofunnel -FUNNEL_VERSION=v0.11.8 +FUNNEL_VERSION=v0.11.12 TesOutputBucketPrefix=s3:// # Output bucket prefix for the TES executing agent to write results to IgnoreHutchSSL=true diff --git a/ServiceStack/compose-manifests/tes/funnel/Dockerfile b/ServiceStack/compose-manifests/tes/funnel/Dockerfile index 5c727d7..a62e74f 100644 --- a/ServiceStack/compose-manifests/tes/funnel/Dockerfile +++ b/ServiceStack/compose-manifests/tes/funnel/Dockerfile @@ -1,13 +1,17 @@ -FROM docker:dind-rootless +FROM golang:1.26-alpine AS builder ARG FUNNEL_VERSION +RUN apk add --no-cache git make bash +WORKDIR /build +RUN git clone https://github.com/calypr/funnel.git . +RUN git checkout tags/${FUNNEL_VERSION} +RUN go build -o bin/funnel . + +FROM docker:dind-rootless + USER root -RUN apk add --no-cache curl perl-utils \ - && sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohsu-comp-bio/funnel/refs/heads/develop/install.sh)" -- ${FUNNEL_VERSION} \ - && cp /root/.local/bin/funnel /usr/local/bin/funnel \ - && chown rootless:rootless /usr/local/bin/funnel \ - && chmod +x /usr/local/bin/funnel \ - && apk del curl perl-utils +COPY --from=builder /build/bin/funnel /usr/local/bin/funnel +RUN chown rootless:rootless /usr/local/bin/funnel && chmod +x /usr/local/bin/funnel USER rootless # Set data dir diff --git a/ServiceStack/compose-manifests/tes/funnel/config.template.yaml b/ServiceStack/compose-manifests/tes/funnel/config.template.yaml index 6656b4a..79d22a8 100644 --- a/ServiceStack/compose-manifests/tes/funnel/config.template.yaml +++ b/ServiceStack/compose-manifests/tes/funnel/config.template.yaml @@ -2,10 +2,6 @@ Database: boltdb Compute: local -Logger: - Level: info - OutputFile: "" - Server: HTTPPort: "8000" RPCPort: "9090" @@ -23,9 +19,6 @@ BoltDB: AmazonS3: Disabled: true - MaxRetries: 10 - Key: "" - Secret: "" GenericS3: - Disabled: false diff --git a/ServiceStack/compose-manifests/tes/tes.yml b/ServiceStack/compose-manifests/tes/tes.yml index 42827ae..bc1b553 100644 --- a/ServiceStack/compose-manifests/tes/tes.yml +++ b/ServiceStack/compose-manifests/tes/tes.yml @@ -1,6 +1,6 @@ services: dind: - image: docker:dind + image: docker:20-dind privileged: true command: dockerd --host=tcp://0.0.0.0:2375 healthcheck: @@ -42,6 +42,7 @@ services: - MinioKey=${FunnelMinioUser} - MinioSecret=${FunnelMinioPass} - DOCKER_HOST=tcp://dind:2375 + - DOCKER_API_VERSION=1.41 networks: - sub-net volumes: