diff --git a/README.md b/README.md index 4fa2c54..90951ed 100644 --- a/README.md +++ b/README.md @@ -41,6 +41,7 @@ bwa|0.7.17-r1188|docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa:0.7.17-r1188 bwa|latest|docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa:latest canvas|1.11.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/canvas:1.11.0 cbio-etl|v2.4.4|docker pull pgc-images.sbgenomics.com/d3b-bixu/cbio-etl:v2.4.4 +cbio-etl|v2.4.6|docker pull pgc-images.sbgenomics.com/d3b-bixu/cbio-etl:v2.4.6 cellranger|3.1|docker pull pgc-images.sbgenomics.com/d3b-bixu/cellranger:3.1 cellranger|5.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/cellranger:5.0 cellranger|6.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/cellranger:6.0 diff --git a/cbio-etl/v2.4.6/Dockerfile b/cbio-etl/v2.4.6/Dockerfile new file mode 100644 index 0000000..4dccd7c --- /dev/null +++ b/cbio-etl/v2.4.6/Dockerfile @@ -0,0 +1,34 @@ +ARG PLATFORM=linux/amd64 +FROM --platform=${PLATFORM} ubuntu:24.04 + +LABEL maintainer="Miguel Brown " +LABEL description="cbio-etl" + +ENV DEBIAN_FRONTEND=noninteractive + +RUN apt update && apt install -y \ + apt-utils \ + git \ + curl \ + vim \ + python3 \ + python3-pip \ + python3-dev \ + pkg-config \ + build-essential \ + bedtools \ + && rm -rf /var/lib/apt/lists/* + +WORKDIR / + +ENV CBIO_ETL_VERSION=2.4.6 +ENV CBIO_REFS_VERSION=1.1.1 + +RUN git clone https://github.com/kids-first/kf-cbioportal-etl.git \ + && cd kf-cbioportal-etl \ + && git checkout v${CBIO_ETL_VERSION} \ + && curl -L https://github.com/kids-first/kf-cbioportal-etl-refs/archive/refs/tags/v${CBIO_REFS_VERSION}.tar.gz | tar -xz -C cbioportal_etl/ --wildcards '*REFS/*' --strip-components=1 \ + && curl -L https://github.com/kids-first/kf-cbioportal-etl-refs/archive/refs/tags/v${CBIO_REFS_VERSION}.tar.gz | tar -xz -C cbioportal_etl/ --wildcards '*STUDY_CONFIGS/*' --strip-components=1 \ + && pip install --break-system-packages . + +COPY Dockerfile .