diff --git a/README.md b/README.md index 2c6ed4c..84eed36 100644 --- a/README.md +++ b/README.md @@ -40,9 +40,7 @@ bwa|0.7.15-r1140|docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa:0.7.15-r1140 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|v2.2.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/cbio-etl:v2.2.0 -cbio-etl|v2.4.1|docker pull pgc-images.sbgenomics.com/d3b-bixu/cbio-etl:v2.4.1 -cbio-etl|v2.4.3|docker pull pgc-images.sbgenomics.com/d3b-bixu/cbio-etl:v2.4.3 +cbio-etl|v2.4.4|docker pull pgc-images.sbgenomics.com/d3b-bixu/cbio-etl:v2.4.4 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/v2.2.0/Dockerfile b/cbio-etl/v2.2.0/Dockerfile deleted file mode 100644 index 12992a0..0000000 --- a/cbio-etl/v2.2.0/Dockerfile +++ /dev/null @@ -1,27 +0,0 @@ -FROM --platform=linux/amd64 ubuntu:22.04 - -LABEL maintainer="Jessica Wong " -LABEL description="cbio-etl" - -RUN apt-get update && apt-get install -y \ - apt-utils \ - curl \ - python3 \ - python3-pip \ - python3-dev \ - pkg-config \ - libmysqlclient-dev \ - build-essential \ - perl \ - libtry-tiny-perl \ - bedtools \ - && rm -rf /var/lib/apt/lists/* - -ENV CBIO_ETL_VERSION 2.2.0 - -WORKDIR / - -RUN curl -L https://github.com/kids-first/kf-cbioportal-etl/archive/refs/tags/v${CBIO_ETL_VERSION}.tar.gz | tar xz \ - && pip install /kf-cbioportal-etl-${CBIO_ETL_VERSION}/ - -COPY Dockerfile . diff --git a/cbio-etl/v2.4.1/Dockerfile b/cbio-etl/v2.4.1/Dockerfile deleted file mode 100644 index b0407e8..0000000 --- a/cbio-etl/v2.4.1/Dockerfile +++ /dev/null @@ -1,34 +0,0 @@ -FROM --platform=linux/amd64 ubuntu:22.04 - -LABEL maintainer="Jessica Wong " -LABEL description="cbio-etl" - -RUN apt-get update && apt-get install -y \ - apt-utils \ - git \ - curl \ - vim \ - python3 \ - python3-pip \ - python3-dev \ - pkg-config \ - libmysqlclient-dev \ - build-essential \ - bedtools \ - && rm -rf /var/lib/apt/lists/* - -RUN python3 -m pip install --upgrade pip setuptools wheel - -WORKDIR / - -ENV CBIO_ETL_VERSION 2.4.1 -ENV CBIO_REFS_VERSION 1.1.0 - -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 . - -COPY Dockerfile . diff --git a/cbio-etl/v2.4.3/Dockerfile b/cbio-etl/v2.4.4/Dockerfile similarity index 97% rename from cbio-etl/v2.4.3/Dockerfile rename to cbio-etl/v2.4.4/Dockerfile index 1d3e6e8..dd69518 100644 --- a/cbio-etl/v2.4.3/Dockerfile +++ b/cbio-etl/v2.4.4/Dockerfile @@ -21,7 +21,7 @@ RUN python3 -m pip install --upgrade pip setuptools wheel WORKDIR / -ENV CBIO_ETL_VERSION=2.4.3 +ENV CBIO_ETL_VERSION=2.4.4 ENV CBIO_REFS_VERSION=1.1.1 RUN git clone https://github.com/kids-first/kf-cbioportal-etl.git \