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Add gzip to image templates #1114

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9a8ae54
Add gzip to image templates
matthdsm Aug 19, 2026
502eb8f
fix copy paste error
matthdsm Aug 19, 2026
c1c8fe6
Update src/main/resources/templates/conda-pixi-v1/dockerfile-conda-fi…
matthdsm Aug 19, 2026
9e4d9b6
add space
ewels Aug 19, 2026
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2 changes: 1 addition & 1 deletion src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt
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Expand Up @@ -2,7 +2,7 @@ FROM {{mamba_image}} AS build
USER root
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
RUN micromamba install -y -n base conda-forge::which \
RUN micromamba install -y -n base conda-forge::which conda-forge::gzip \
&& ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \
&& (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \
&& cat /tmp/mamba.log \
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2 changes: 1 addition & 1 deletion src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt
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Expand Up @@ -2,7 +2,7 @@ FROM {{mamba_image}} AS build
USER root
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
RUN \
micromamba install -y -n base conda-forge::which \
micromamba install -y -n base conda-forge::which conda-forge::gzip \
&& ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \
&& (micromamba install -y -n base {{channel_opts}} {{target}} > /tmp/mamba.log 2>&1 \
&& cat /tmp/mamba.log \
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2 changes: 1 addition & 1 deletion src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt
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Expand Up @@ -4,7 +4,7 @@ From: {{mamba_image}}
{{wave_context_dir}}/conda.yml /scratch/conda.yml
%post
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
micromamba install -y -n base conda-forge::which
micromamba install -y -n base conda-forge::which conda-forge::gzip
ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which
micromamba install -y -n base -f /scratch/conda.yml > /tmp/mamba.log 2>&1 \
&& cat /tmp/mamba.log \
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2 changes: 1 addition & 1 deletion src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-packages.txt
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Expand Up @@ -2,7 +2,7 @@ BootStrap: docker
From: {{mamba_image}}
%post
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
micromamba install -y -n base conda-forge::which
micromamba install -y -n base conda-forge::which conda-forge::gzip
ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which
micromamba install -y -n base {{channel_opts}} {{target}} > /tmp/mamba.log 2>&1 \
&& cat /tmp/mamba.log \
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2 changes: 1 addition & 1 deletion src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt
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Expand Up @@ -4,7 +4,7 @@ COPY conda.yml /opt/wave/conda.yml
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \
&& pixi add conda-forge::which \
&& pixi add conda-forge::which conda-forge::gzip \
{{base_packages}}
&& pixi shell-hook > /shell-hook.sh \
&& echo 'exec "$@"' >> /shell-hook.sh \
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2 changes: 1 addition & 1 deletion src/main/resources/templates/conda-pixi-v1/singularityfile-conda-file.txt
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Expand Up @@ -5,7 +5,7 @@ From: {{pixi_image}}
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
pixi add conda-forge::which conda-forge::gzip
{{base_packages}}
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
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