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🐳 cbio 2.4.8 image #298

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Merged
migbro merged 3 commits into from
Mar 19, 2026
Merged

🐳 cbio 2.4.8 image #298

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f585805
:whale: cbio 2.4.8 image
migbro Mar 12, 2026
f1274af
:hammer: update 2.4.6 as it has same pre-reqs
migbro Mar 12, 2026
ee973c6
update docker table (#299)
github-actions[bot] Mar 12, 2026
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -43,6 +43,7 @@ canvas|1.11.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/canvas:1.11.0
cbio-etl-base|v1.0.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/cbio-etl-base:v1.0.0
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
cbio-etl|v2.4.8|docker pull pgc-images.sbgenomics.com/d3b-bixu/cbio-etl:v2.4.8
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
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15 changes: 1 addition & 14 deletions cbio-etl/v2.4.6/Dockerfile
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@@ -1,24 +1,11 @@
ARG PLATFORM=linux/amd64
FROM --platform=${PLATFORM} ubuntu:24.04
FROM --platform=${PLATFORM} pgc-images.sbgenomics.com/d3b-bixu/cbio-etl-base:v1.0.0

LABEL maintainer="Miguel Brown <brownm28@chop.edu>"
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
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21 changes: 21 additions & 0 deletions cbio-etl/v2.4.8/Dockerfile
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@@ -0,0 +1,21 @@
ARG PLATFORM=linux/amd64
FROM --platform=${PLATFORM} pgc-images.sbgenomics.com/d3b-bixu/cbio-etl-base:v1.0.0

LABEL maintainer="Miguel Brown <brownm28@chop.edu>"
LABEL description="cbio-etl"

ENV DEBIAN_FRONTEND=noninteractive

WORKDIR /

ENV CBIO_ETL_VERSION=2.4.8
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 .
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