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RW-12661 update qiime #502

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fb35084
update qiime
Qi77Qi Feb 24, 2025
7856d2d
adding qimme
Qi77Qi Mar 7, 2025
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comments
Qi77Qi Mar 10, 2025
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version
Qi77Qi Mar 10, 2025
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add script
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more
Qi77Qi Mar 11, 2025
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update
Qi77Qi Mar 11, 2025
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remove docker
Qi77Qi Mar 11, 2025
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try sth
Qi77Qi Mar 11, 2025
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Qi77Qi Mar 11, 2025
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try
Qi77Qi Mar 11, 2025
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Qi77Qi Mar 13, 2025
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Qi77Qi Mar 14, 2025
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Qi77Qi Mar 17, 2025
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10 changes: 6 additions & 4 deletions terra-jupyter-aou/Dockerfile
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Expand Up @@ -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 \
Expand All @@ -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 && \
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4 changes: 4 additions & 0 deletions terra-rstudio-aou/CHANGELOG.md
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@@ -1,5 +1,9 @@
# Changelog

## 0.1.2 - 2025-03-07
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@LizBaldo LizBaldo Mar 10, 2025

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Should this changelog and version control be for terra-jupyter-aou instead? I am alsways a bit confused about version control since there is a single image for both jupyter and r.

Would you be able to update the conf.json file accordingly?

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@Qi77Qi Qi77Qi Mar 10, 2025

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oh yea...updated the wrong file..good catch!

* upgrade qiime
* install qiime2R

## 0.1.1 - 2023-03-16

* Install Wondershaper
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2 changes: 1 addition & 1 deletion terra-rstudio-aou/VERSION
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@@ -1 +1 @@
0.1.1
0.1.2