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Use conda-lock to generate environment.lock (closes #975) #1063

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edbdaaa
Use conda-lock to generate environment.lock so pip deps are included
munishchouhan Jun 25, 2026
d9b48c9
Invoke conda-lock via `micromamba run -n base`
munishchouhan Jun 25, 2026
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3 changes: 2 additions & 1 deletion src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt
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Expand Up @@ -2,7 +2,8 @@ FROM {{base_image}}
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN micromamba install -y -n base -f /tmp/conda.yml \
{{base_packages}}
&& micromamba env export --name base --explicit > environment.lock \
&& micromamba install -y -n base conda-forge::conda-lock \
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \
&& echo ">> CONDA_LOCK_START" \
&& cat environment.lock \
&& echo "<< CONDA_LOCK_END" \
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3 changes: 2 additions & 1 deletion src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt
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Expand Up @@ -5,7 +5,8 @@ From: {{base_image}}
%post
micromamba install -y -n base -f /scratch/conda.yml
{{base_packages}}
micromamba env export --name base --explicit > environment.lock
micromamba install -y -n base conda-forge::conda-lock
micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
echo "<< CONDA_LOCK_END"
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3 changes: 2 additions & 1 deletion src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt
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Expand Up @@ -5,8 +5,9 @@ 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 install -y -n base conda-forge::conda-lock \
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \
&& micromamba clean -a -y \
&& micromamba env export --name base --explicit > environment.lock \
&& echo ">> CONDA_LOCK_START" \
&& cat environment.lock \
&& echo "<< CONDA_LOCK_END"
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3 changes: 2 additions & 1 deletion src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt
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Expand Up @@ -8,8 +8,9 @@ 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 install -y -n base conda-forge::conda-lock
micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
echo "<< CONDA_LOCK_END"
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15 changes: 10 additions & 5 deletions src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy
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Expand Up @@ -123,7 +123,8 @@ class ContainerHelperTest extends Specification {
%post
micromamba install -y -n base -f /scratch/conda.yml
micromamba install -y -n base foo::one bar::two
micromamba env export --name base --explicit > environment.lock
micromamba install -y -n base conda-forge::conda-lock
micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
echo "<< CONDA_LOCK_END"
Expand All @@ -150,7 +151,8 @@ class ContainerHelperTest extends Specification {
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN micromamba install -y -n base -f /tmp/conda.yml \\
&& micromamba install -y -n base foo::one bar::two \\
&& micromamba env export --name base --explicit > environment.lock \\
&& micromamba install -y -n base conda-forge::conda-lock \\
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END" \\
Expand Down Expand Up @@ -736,8 +738,9 @@ 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 install -y -n base conda-forge::conda-lock \\
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END"
Expand Down Expand Up @@ -774,8 +777,9 @@ 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 install -y -n base conda-forge::conda-lock \\
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END"
Expand Down Expand Up @@ -817,8 +821,9 @@ 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 install -y -n base conda-forge::conda-lock \\
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END"
Expand Down
24 changes: 16 additions & 8 deletions src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy
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Expand Up @@ -37,7 +37,8 @@ class TemplateUtilsTest extends Specification {
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN micromamba install -y -n base -f /tmp/conda.yml \\
&& micromamba install -y -n base foo::bar \\
&& micromamba env export --name base --explicit > environment.lock \\
&& micromamba install -y -n base conda-forge::conda-lock \\
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END" \\
Expand All @@ -55,7 +56,8 @@ class TemplateUtilsTest extends Specification {
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN micromamba install -y -n base -f /tmp/conda.yml \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba env export --name base --explicit > environment.lock \\
&& micromamba install -y -n base conda-forge::conda-lock \\
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END" \\
Expand Down Expand Up @@ -196,7 +198,8 @@ class TemplateUtilsTest extends Specification {
%post
micromamba install -y -n base -f /scratch/conda.yml
micromamba install -y -n base foo::bar=1.0
micromamba env export --name base --explicit > environment.lock
micromamba install -y -n base conda-forge::conda-lock
micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
echo "<< CONDA_LOCK_END"
Expand All @@ -217,7 +220,8 @@ class TemplateUtilsTest extends Specification {
%post
micromamba install -y -n base -f /scratch/conda.yml
micromamba install -y -n base conda-forge::procps-ng
micromamba env export --name base --explicit > environment.lock
micromamba install -y -n base conda-forge::conda-lock
micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
echo "<< CONDA_LOCK_END"
Expand Down Expand Up @@ -488,8 +492,9 @@ 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 install -y -n base conda-forge::conda-lock \\
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END"
Expand All @@ -513,8 +518,9 @@ 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 install -y -n base conda-forge::conda-lock \\
&& micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\
&& micromamba clean -a -y \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<< CONDA_LOCK_END"
Expand Down Expand Up @@ -774,8 +780,9 @@ 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 install -y -n base conda-forge::conda-lock
micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
echo "<< CONDA_LOCK_END"
Expand All @@ -799,8 +806,9 @@ 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 install -y -n base conda-forge::conda-lock
micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock
micromamba clean -a -y
micromamba env export --name base --explicit > environment.lock
echo ">> CONDA_LOCK_START"
cat environment.lock
echo "<< CONDA_LOCK_END"
Expand Down
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