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fix: make which available for R (bioconda) post-links in conda v2 builds #1070

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Merged
pditommaso merged 1 commit into from
Jul 6, 2026
Merged

fix: make which available for R (bioconda) post-links in conda v2 builds #1070

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6 changes: 5 additions & 1 deletion src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt
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@@ -1,6 +1,10 @@
FROM {{mamba_image}} AS build
USER root
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \
# 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 "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \
&& (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \
&& cat /tmp/mamba.log \
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \
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6 changes: 5 additions & 1 deletion src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-packages.txt
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@@ -1,6 +1,10 @@
FROM {{mamba_image}} AS build
USER root
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
RUN \
(micromamba install -y -n base {{channel_opts}} {{target}} > /tmp/mamba.log 2>&1 \
micromamba install -y -n base conda-forge::which \
&& ln -sf "$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 \
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base {{channel_opts}} {{target}})) \
Expand Down
3 changes: 3 additions & 0 deletions src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt
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Expand Up @@ -3,6 +3,9 @@ From: {{mamba_image}}
%files
{{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
ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which
micromamba install -y -n base -f /scratch/conda.yml > /tmp/mamba.log 2>&1 \
&& cat /tmp/mamba.log \
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \
Expand Down
3 changes: 3 additions & 0 deletions src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-packages.txt
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@@ -1,6 +1,9 @@
BootStrap: docker
From: {{mamba_image}}
%post
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
micromamba install -y -n base conda-forge::which
ln -sf "$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 \
Expand Down
1 change: 1 addition & 0 deletions src/main/resources/templates/conda-pixi-v1/dockerfile-conda-file.txt
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Expand Up @@ -4,6 +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 \
{{base_packages}}
&& pixi shell-hook > /shell-hook.sh \
&& echo 'exec "$@"' >> /shell-hook.sh \
Expand Down
1 change: 1 addition & 0 deletions src/main/resources/templates/conda-pixi-v1/singularityfile-conda-file.txt
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Expand Up @@ -5,6 +5,7 @@ From: {{pixi_image}}
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
{{base_packages}}
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
Expand Down
26 changes: 22 additions & 4 deletions src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy
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Expand Up @@ -634,6 +634,7 @@ class ContainerHelperTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add conda-forge::procps-ng \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
Expand Down Expand Up @@ -686,6 +687,7 @@ class ContainerHelperTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add foo::one bar::two \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
Expand Down Expand Up @@ -730,8 +732,12 @@ class ContainerHelperTest extends Specification {
then:
result =='''\
FROM mambaorg/micromamba:2-amazon2023 AS build
USER root
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
RUN micromamba install -y -n base conda-forge::which \\
&& ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \\
&& (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
Expand Down Expand Up @@ -768,8 +774,12 @@ class ContainerHelperTest extends Specification {
then:
result =='''\
FROM mambaorg/micromamba:2-amazon2023 AS build
USER root
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
# 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 "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \\
&& (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
Expand Down Expand Up @@ -811,8 +821,12 @@ class ContainerHelperTest extends Specification {
then:
result =='''\
FROM mambaorg/micromamba:2.0.0 AS build
USER root
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
RUN micromamba install -y -n base conda-forge::which \\
&& ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \\
&& (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
Expand Down Expand Up @@ -848,8 +862,12 @@ class ContainerHelperTest extends Specification {
then:
result =='''\
FROM mambaorg/micromamba:2-amazon2023 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 -c conda-forge -c bioconda -f https://foo.com/lock.yml > /tmp/mamba.log 2>&1 \\
micromamba install -y -n base conda-forge::which \\
&& ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \\
&& (micromamba install -y -n base -c conda-forge -c bioconda -f https://foo.com/lock.yml > /tmp/mamba.log 2>&1 \\
&& 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 -c bioconda -f https://foo.com/lock.yml)) \\
Expand Down
42 changes: 38 additions & 4 deletions src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy
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Expand Up @@ -358,6 +358,7 @@ class TemplateUtilsTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add foo::bar \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
Expand Down Expand Up @@ -393,6 +394,7 @@ class TemplateUtilsTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add conda-forge::procps-ng \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
Expand Down Expand Up @@ -431,6 +433,7 @@ class TemplateUtilsTest extends Specification {
WORKDIR /opt/wave

RUN pixi init --import /opt/wave/conda.yml \\
&& pixi add conda-forge::which \\
&& pixi add conda-forge::procps-ng \\
&& pixi shell-hook > /shell-hook.sh \\
&& echo 'exec "$@"' >> /shell-hook.sh \\
Expand Down Expand Up @@ -482,8 +485,12 @@ class TemplateUtilsTest extends Specification {
expect:
TemplateUtils.condaFileToDockerFileUsingV2(CONDA_OPTS) == '''\
FROM mambaorg/micromamba:2.1.1 AS build
USER root
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
RUN micromamba install -y -n base conda-forge::which \\
&& ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \\
&& (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
Expand All @@ -507,8 +514,12 @@ class TemplateUtilsTest extends Specification {
expect:
TemplateUtils.condaFileToDockerFileUsingV2(new CondaOpts([:])) == '''\
FROM mambaorg/micromamba:1.5.10-noble AS build
USER root
COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
# 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 "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \\
&& (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\
Expand Down Expand Up @@ -541,8 +552,12 @@ class TemplateUtilsTest extends Specification {
expect:
TemplateUtils.condaPackagesToDockerFileUsingV2(PACKAGES, CHANNELS, CONDA_OPTS) == '''\
FROM mambaorg/micromamba:2.1.1 AS build
USER root
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
RUN \\
(micromamba install -y -n base -c conda-forge -c bioconda bwa=0.7.15 salmon=1.1.1 > /tmp/mamba.log 2>&1 \\
micromamba install -y -n base conda-forge::which \\
&& ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \\
&& (micromamba install -y -n base -c conda-forge -c bioconda bwa=0.7.15 salmon=1.1.1 > /tmp/mamba.log 2>&1 \\
&& 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 -c bioconda bwa=0.7.15 salmon=1.1.1)) \\
Expand Down Expand Up @@ -575,8 +590,12 @@ class TemplateUtilsTest extends Specification {
expect:
TemplateUtils.condaPackagesToDockerFileUsingV2(PACKAGES, CHANNELS, CONDA_OPTS) == '''\
FROM mambaorg/micromamba:2.1.1 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 -c conda-forge numpy pandas > /tmp/mamba.log 2>&1 \\
micromamba install -y -n base conda-forge::which \\
&& ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which \\
&& (micromamba install -y -n base -c conda-forge numpy pandas > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
&& CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -c conda-forge numpy pandas)) \\
Expand Down Expand Up @@ -665,6 +684,7 @@ class TemplateUtilsTest extends Specification {
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
pixi add conda-forge::procps-ng
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
Expand All @@ -685,6 +705,7 @@ class TemplateUtilsTest extends Specification {
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
pixi add conda-forge::procps-ng
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
Expand Down Expand Up @@ -712,6 +733,7 @@ class TemplateUtilsTest extends Specification {
%post
mkdir /opt/wave && cd /opt/wave
pixi init --import /scratch/conda.yml
pixi add conda-forge::which
pixi shell-hook > /shell-hook.sh
echo ">> CONDA_LOCK_START"
cat /opt/wave/pixi.lock
Expand Down Expand Up @@ -769,6 +791,9 @@ class TemplateUtilsTest extends Specification {
%files
{{wave_context_dir}}/conda.yml /scratch/conda.yml
%post
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
micromamba install -y -n base conda-forge::which
ln -sf "$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 \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
Expand All @@ -794,6 +819,9 @@ class TemplateUtilsTest extends Specification {
%files
{{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
ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which
micromamba install -y -n base -f /scratch/conda.yml > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
Expand Down Expand Up @@ -825,6 +853,9 @@ class TemplateUtilsTest extends Specification {
BootStrap: docker
From: mambaorg/micromamba:2.1.1
%post
# expose `which` at /usr/bin/which for R (bioconda) post-link scripts; the amazon2023 base image lacks it
micromamba install -y -n base conda-forge::which
ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which
micromamba install -y -n base -c conda-forge -c bioconda bwa=0.7.15 salmon=1.1.1 > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
Expand Down Expand Up @@ -856,6 +887,9 @@ class TemplateUtilsTest extends Specification {
BootStrap: docker
From: mambaorg/micromamba:2.1.1
%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
ln -sf "$MAMBA_ROOT_PREFIX/bin/which" /usr/bin/which
micromamba install -y -n base -c conda-forge numpy pandas > /tmp/mamba.log 2>&1 \\
&& cat /tmp/mamba.log \\
|| (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\
Expand Down
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