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fix: add micromamba clean to v2 templates to reduce image size #1038

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Merged
munishchouhan merged 1 commit into from
Apr 27, 2026
Merged

fix: add micromamba clean to v2 templates to reduce image size #1038

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1 change: 1 addition & 0 deletions src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt
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Expand Up @@ -5,6 +5,7 @@ RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \
{{base_packages}}
&& micromamba clean -a -y \
&& micromamba env export --name base --explicit > environment.lock \
&& echo ">> CONDA_LOCK_START" \
&& cat environment.lock \
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1 change: 1 addition & 0 deletions src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt
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Expand Up @@ -5,6 +5,7 @@ RUN \
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base {{channel_opts}} {{target}})) \
{{base_packages}}
&& micromamba clean -a -y \
&& micromamba env export --name base --explicit > environment.lock \
&& echo ">> CONDA_LOCK_START" \
&& cat environment.lock \
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1 change: 1 addition & 0 deletions src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt
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Expand Up @@ -8,6 +8,7 @@ From: {{mamba_image}}
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml)
{{base_packages}}
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
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1 change: 1 addition & 0 deletions src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-packages.txt
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Expand Up @@ -6,6 +6,7 @@ From: {{mamba_image}}
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base {{channel_opts}} {{target}})
{{base_packages}}
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
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3 changes: 3 additions & 0 deletions src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy
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Expand Up @@ -736,6 +736,7 @@ class ContainerHelperTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
Expand Down Expand Up @@ -778,6 +779,7 @@ class ContainerHelperTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
&& micromamba install -y -n base foo::one bar::two \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
Expand Down Expand Up @@ -814,6 +816,7 @@ class ContainerHelperTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -c conda-forge -c bioconda -f https://foo.com/lock.yml)) \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
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8 changes: 8 additions & 0 deletions src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy
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Expand Up @@ -488,6 +488,7 @@ class TemplateUtilsTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
Expand All @@ -512,6 +513,7 @@ class TemplateUtilsTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
Expand Down Expand Up @@ -545,6 +547,7 @@ class TemplateUtilsTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -c conda-forge -c bioconda bwa=0.7.15 salmon=1.1.1)) \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
Expand Down Expand Up @@ -577,6 +580,7 @@ class TemplateUtilsTest extends Specification {
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -c conda-forge numpy pandas)) \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
Expand Down Expand Up @@ -770,6 +774,7 @@ class TemplateUtilsTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml)
micromamba install -y -n base conda-forge::procps-ng
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
Expand All @@ -794,6 +799,7 @@ class TemplateUtilsTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml)
micromamba install -y -n base conda-forge::procps-ng
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
Expand Down Expand Up @@ -824,6 +830,7 @@ class TemplateUtilsTest extends Specification {
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -c conda-forge -c bioconda bwa=0.7.15 salmon=1.1.1)
micromamba install -y -n base conda-forge::procps-ng
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
Expand Down Expand Up @@ -853,6 +860,7 @@ class TemplateUtilsTest extends Specification {
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -c conda-forge numpy pandas)
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
Expand Down
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