diff --git a/.github/workflows/test-terra-jupyter-aou.yml b/.github/workflows/test-terra-jupyter-aou.yml index 2d5dc55d..39c2eb59 100644 --- a/.github/workflows/test-terra-jupyter-aou.yml +++ b/.github/workflows/test-terra-jupyter-aou.yml @@ -38,7 +38,7 @@ env: jobs: test_docker_image: - runs-on: self-hosted + runs-on: ubuntu-latest steps: - name: Checkout diff --git a/config/conf.json b/config/conf.json index 3024a9a6..cdfdc133 100644 --- a/config/conf.json +++ b/config/conf.json @@ -137,7 +137,7 @@ "packages" : { }, - "version" : "2.1.9", + "version" : "2.1.9.2", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index fa7ee8d2..4b7c1863 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,11 +1,3 @@ -## 2.1.9 - 2022-09-02 - - - Add support for QIIME2 - - Update `hail` to `0.2.98` - - See https://hail.is/docs/0.2/change_log.html#version-0-2-98) for details - -Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.1.9` - ## 2.1.8 - 2022-07-12 - Revert attempted Java11 upgrade back to Java8 diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index c23c7378..cf1c1a6b 100644 --- a/terra-jupyter-aou/Dockerfile +++ b/terra-jupyter-aou/Dockerfile @@ -47,7 +47,7 @@ RUN jupyter nbextension enable --py igv --sys-prefix ENV PYTHONPATH $PYTHONPATH:/usr/lib/spark/python ENV PYSPARK_PYTHON=python3 -ENV HAIL_VERSION=0.2.98 +ENV HAIL_VERSION=0.2.96 RUN find $JUPYTER_HOME/scripts -name '*.sh' -type f | xargs chmod +x \ && $JUPYTER_HOME/scripts/kernel/kernelspec.sh $JUPYTER_HOME/scripts/kernel /opt/conda/share/jupyter/kernels \ @@ -193,11 +193,5 @@ RUN R -e 'BiocManager::install(c("GENESIS"))' ENV R_LIBS /usr/local/lib/R/site-library:/opt/conda/lib/R/library RUN conda install -c bioconda r-saige -# RW-8725 INSTALL QIMEE2 -RUN curl -L -o qiime2-2022.8.yml https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml && \ - conda env create -n qiime2-2022.8 --file qiime2-2022.8.yml && \ - rm qiime2-2022.8.yml - - ENV PIP_USER=true USER $USER