From 9a8ae54043b0bc591ddba330542837acf635cf69 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 19 Aug 2026 10:18:30 +0200 Subject: [PATCH 1/4] Add gzip to image templates --- .../templates/conda-micromamba-v2/dockerfile-conda-file.txt | 2 +- .../templates/conda-micromamba-v2/dockerfile-conda-packages.txt | 2 +- .../conda-micromamba-v2/singularityfile-conda-file.txt | 2 +- .../conda-micromamba-v2/singularityfile-conda-packages.txt | 2 +- .../resources/templates/conda-pixi-v1/dockerfile-conda-file.txt | 2 +- .../templates/conda-pixi-v1/singularityfile-conda-file.txt | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt index 045faf01b..0b30e41e7 100644 --- a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt @@ -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 "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \ && (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \ && cat /tmp/mamba.log \ diff --git a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt index 50b2e1ca1..42d669151 100644 --- a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt +++ b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt @@ -3,7 +3,7 @@ USER root # expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it RUN \ micromamba install -y -n base conda-forge::which \ - && ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \ + && ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which conda-forge::gzip\ && (micromamba install -y -n base {{channel_opts}} {{target}} > /tmp/mamba.log 2>&1 \ && cat /tmp/mamba.log \ || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \ diff --git a/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt index 95de21b96..81fa2cf9c 100644 --- a/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt @@ -4,7 +4,7 @@ From: {{mamba_image}} {{wave_context_dir}}/conda.yml /scratch/conda.yml %post # expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it - micromamba install -y -n base conda-forge::which + micromamba install -y -n base conda-forge::which conda-forge::gzip ln -sf "$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 \ diff --git a/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-packages.txt b/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-packages.txt index 14c49e017..b2bea7bb8 100644 --- a/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-packages.txt +++ b/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-packages.txt @@ -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 "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which micromamba install -y -n base {{channel_opts}} {{target}} > /tmp/mamba.log 2>&1 \ && cat /tmp/mamba.log \ diff --git a/src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt b/src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt index 49fac3371..d3446d674 100644 --- a/src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt +++ b/src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt @@ -4,7 +4,7 @@ COPY conda.yml /opt/wave/conda.yml WORKDIR /opt/wave RUN pixi init --import /opt/wave/conda.yml \ - && pixi add conda-forge::which \ + && pixi add conda-forge::which conda-forge::gzip\ {{base_packages}} && pixi shell-hook > /shell-hook.sh \ && echo 'exec "$@"' >> /shell-hook.sh \ diff --git a/src/main/resources/templates/conda-pixi-v1/singularityfile-conda-file.txt b/src/main/resources/templates/conda-pixi-v1/singularityfile-conda-file.txt index 8c5a3d856..e676165bc 100644 --- a/src/main/resources/templates/conda-pixi-v1/singularityfile-conda-file.txt +++ b/src/main/resources/templates/conda-pixi-v1/singularityfile-conda-file.txt @@ -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" From 502eb8ff5507a403ad7bbd37b205ca71445db66f Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 19 Aug 2026 10:21:58 +0200 Subject: [PATCH 2/4] fix copy paste error --- .../conda-micromamba-v2/dockerfile-conda-packages.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt index 42d669151..44a514cd0 100644 --- a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt +++ b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt @@ -2,8 +2,8 @@ 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 \ - && ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which conda-forge::gzip\ + micromamba install -y -n base conda-forge::which conda-forge::gzip\ + && ln -sf "$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 \ || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \ From c1c8fe612deb9c511d9f5a0f7ef6b643372a96b2 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 19 Aug 2026 10:22:50 +0200 Subject: [PATCH 3/4] Update src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt Co-authored-by: Phil Ewels --- .../resources/templates/conda-pixi-v1/dockerfile-conda-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt b/src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt index d3446d674..286387f4c 100644 --- a/src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt +++ b/src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt @@ -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 conda-forge::gzip\ + && pixi add conda-forge::which conda-forge::gzip \ {{base_packages}} && pixi shell-hook > /shell-hook.sh \ && echo 'exec "$@"' >> /shell-hook.sh \ From 9e4d9b6e787858d11529d7ad9741c756c5d215d7 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 19 Aug 2026 10:38:25 +0200 Subject: [PATCH 4/4] add space --- .../templates/conda-micromamba-v2/dockerfile-conda-packages.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt index 44a514cd0..3d066c231 100644 --- a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt +++ b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt @@ -2,7 +2,7 @@ FROM {{mamba_image}} AS build USER root # expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it RUN \ - micromamba install -y -n base conda-forge::which conda-forge::gzip\ + micromamba install -y -n base conda-forge::which conda-forge::gzip \ && ln -sf "$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 \