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Signed-off-by: munishchouhan <[email protected]>
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@munishchouhan
munishchouhan committed Oct 4, 2024
1 parent 3d2fd40 commit e8f4c2d
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Showing 3 changed files with 27 additions and 45 deletions.
8 changes: 3 additions & 5 deletions wave-utils/src/main/resources/templates/conda/dockerfile-conda-file.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,10 @@ 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

RUN echo ">>>>>>> CONDA_LOCK_START" \
&& micromamba env export --name base --explicit > environment.lock \
&& echo ">>>>>>> CONDA_LOCK_START" \
&& cat environment.lock \
&& echo "<<<<<<< CONDA_LOCK_END"

RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
8 changes: 3 additions & 5 deletions wave-utils/src/main/resources/templates/conda/dockerfile-conda-packages.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,10 @@ FROM {{base_image}}
RUN \
micromamba install -y -n base {{channel_opts}} {{target}} \
{{base_packages}}
&& micromamba env export --name base --explicit > environment.lock

RUN echo ">>>>>>> CONDA_LOCK_START" \
&& micromamba env export --name base --explicit > environment.lock \
&& echo ">>>>>>> CONDA_LOCK_START" \
&& cat environment.lock \
&& echo "<<<<<<< CONDA_LOCK_END"

RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
56 changes: 21 additions & 35 deletions wave-utils/src/test/groovy/io/seqera/wave/util/DockerHelperTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -374,13 +374,11 @@ class DockerHelperTest 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
RUN echo ">>>>>>> CONDA_LOCK_START" \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">>>>>>> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<<<<<<< CONDA_LOCK_END"
RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
'''.stripIndent()
Expand All @@ -394,13 +392,11 @@ class DockerHelperTest 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
RUN echo ">>>>>>> CONDA_LOCK_START" \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">>>>>>> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<<<<<<< CONDA_LOCK_END"
RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
'''.stripIndent()
Expand All @@ -417,13 +413,11 @@ class DockerHelperTest extends Specification {
RUN \\
micromamba install -y -n base -c conda-forge -c defaults bwa=0.7.15 salmon=1.1.1 \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba env export --name base --explicit > environment.lock
RUN echo ">>>>>>> CONDA_LOCK_START" \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">>>>>>> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<<<<<<< CONDA_LOCK_END"
RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
'''.stripIndent()
Expand All @@ -441,13 +435,11 @@ class DockerHelperTest extends Specification {
RUN \\
micromamba install -y -n base -c conda-forge -c defaults bwa=0.7.15 salmon=1.1.1 \\
&& micromamba install -y -n base foo::one bar::two \\
&& micromamba env export --name base --explicit > environment.lock
RUN echo ">>>>>>> CONDA_LOCK_START" \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">>>>>>> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<<<<<<< CONDA_LOCK_END"
RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
'''.stripIndent()
Expand All @@ -464,13 +456,11 @@ class DockerHelperTest extends Specification {
RUN \\
micromamba install -y -n base -c foo -c bar bwa=0.7.15 salmon=1.1.1 \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba env export --name base --explicit > environment.lock
RUN echo ">>>>>>> CONDA_LOCK_START" \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">>>>>>> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<<<<<<< CONDA_LOCK_END"
RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
'''.stripIndent()
Expand All @@ -488,13 +478,11 @@ class DockerHelperTest extends Specification {
RUN \\
micromamba install -y -n base -c conda-forge -c defaults bwa=0.7.15 salmon=1.1.1 \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba env export --name base --explicit > environment.lock
RUN echo ">>>>>>> CONDA_LOCK_START" \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">>>>>>> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<<<<<<< CONDA_LOCK_END"
RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
USER my-user
Expand All @@ -515,13 +503,11 @@ class DockerHelperTest extends Specification {
RUN \\
micromamba install -y -n base -c conda-forge -c defaults -f https://foo.com/some/conda-lock.yml \\
&& micromamba install -y -n base conda-forge::procps-ng \\
&& micromamba env export --name base --explicit > environment.lock
RUN echo ">>>>>>> CONDA_LOCK_START" \\
&& micromamba env export --name base --explicit > environment.lock \\
&& echo ">>>>>>> CONDA_LOCK_START" \\
&& cat environment.lock \\
&& echo "<<<<<<< CONDA_LOCK_END"
RUN micromamba clean -a -y
&& micromamba clean -a -y
USER root
ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
USER my-user
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