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Revert "RW-8725 Add QIMEE2 to Jupyter VM Image (#351)" #359

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Revert "RW-8725 Add QIMEE2 to Jupyter VM Image (#351)" #359

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2 changes: 1 addition & 1 deletion .github/workflows/test-terra-jupyter-aou.yml
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Expand Up @@ -38,7 +38,7 @@ env:
jobs:

test_docker_image:
runs-on: self-hosted
runs-on: ubuntu-latest

steps:
- name: Checkout
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2 changes: 1 addition & 1 deletion config/conf.json
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Expand Up @@ -137,7 +137,7 @@
"packages" : {

},
"version" : "2.1.9",
"version" : "2.1.9.2",
"automated_flags" : {
"include_in_ui" : false,
"generate_docs" : false,
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8 changes: 0 additions & 8 deletions terra-jupyter-aou/CHANGELOG.md
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@@ -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
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8 changes: 1 addition & 7 deletions terra-jupyter-aou/Dockerfile
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Expand Up @@ -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 \
Expand Down Expand Up @@ -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