RW-12661 update qiime

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,

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`

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 && \

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