diff --git a/config/conf.json b/config/conf.json index 4ddc34bc..fab3d867 100644 --- a/config/conf.json +++ b/config/conf.json @@ -143,7 +143,7 @@ "packages" : { }, - "version" : "2.2.14", + "version" : "2.2.15-rc1", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index c400e652..eae7c541 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.2.15 - 2025-03-07 +* upgrade qiime +* install qiime2R + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.15` + ## 2.2.14 - 2024-12-04T17:30:49.302274524Z - Update `terra-jupyter-r` to `2.2.6` diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index aa5f471d..7cf7361a 100644 --- a/terra-jupyter-aou/Dockerfile +++ b/terra-jupyter-aou/Dockerfile @@ -186,6 +186,8 @@ RUN R -e 'BiocManager::install(c("GENESIS"))' RUN R -e 'BiocManager::install(c("SAIGEgds","SNPRelate"))' +RUN R -e 'BiocManager::install(c("jbisanz/qiime2R"))' + # Install hdf5 library and h5py RUN apt-get update && \ apt install -yq --no-install-recommends \ @@ -195,10 +197,10 @@ RUN apt-get update && \ && rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && pip install --verbose h5py -# QIIME 2 2024.5 Amplicon Distribution -RUN curl -fsSL -o qiime2-2024.5.yml https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml && \ - conda env create -n qiime2-2024.5 --file qiime2-2024.5.yml && \ - rm qiime2-2024.5.yml +# QIIME 2 2024.10 Amplicon Distribution +RUN curl -fsSL -o qiime2-2024.10.yml https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml && \ + conda env create -n qiime2-2024.10 --file qiime2-2024.10.yml && \ + rm qiime2-2024.10.yml # Install jellyfish RUN mkdir -p /tmp/jellyfish && \ diff --git a/terra-jupyter-aou/upgrade_jupyter_server.sh b/terra-jupyter-aou/upgrade_jupyter_server.sh new file mode 100644 index 00000000..5a9ffd5a --- /dev/null +++ b/terra-jupyter-aou/upgrade_jupyter_server.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +set -e -x + +chown -R jupyter:users $JUPYTER_USER_HOME/ +sudo -E -u jupyter /opt/conda/bin/pip install --upgrade jupyter-server +chown -R jupyter:users /opt/conda/etc/jupyter/ +sudo -E -u jupyter /opt/conda/bin/jupyter server extension enable --py qiime2 --sys-prefix