Export Mamba root path in docker container

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
seqeralabs · Oct 30, 2023 · 348cf29 · 348cf29
1 parent f2948e1
commit 348cf29
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diff --git a/wave-utils/src/main/resources/templates/conda/dockerfile-conda-file.txt b/wave-utils/src/main/resources/templates/conda/dockerfile-conda-file.txt
@@ -4,3 +4,4 @@ RUN micromamba install -y -n base -f /tmp/conda.yml \
     {{base_packages}}
     && micromamba clean -a -y
 USER root
+ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
diff --git a/wave-utils/src/main/resources/templates/conda/dockerfile-conda-packages.txt b/wave-utils/src/main/resources/templates/conda/dockerfile-conda-packages.txt
@@ -4,3 +4,4 @@ RUN \
     {{base_packages}}
     && micromamba clean -a -y
 USER root
+ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
diff --git a/wave-utils/src/test/groovy/io/seqera/wave/util/DockerHelperTest.groovy b/wave-utils/src/test/groovy/io/seqera/wave/util/DockerHelperTest.groovy
@@ -216,6 +216,7 @@ class DockerHelperTest extends Specification {
                     && micromamba install -y -n base foo::bar \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
     }
 
@@ -229,6 +230,7 @@ class DockerHelperTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
     }
 
@@ -245,6 +247,7 @@ class DockerHelperTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
     }
 
@@ -262,6 +265,7 @@ class DockerHelperTest extends Specification {
                     && micromamba install -y -n base foo::one bar::two \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
     }
 
@@ -278,6 +282,7 @@ class DockerHelperTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
     }
 
@@ -295,6 +300,7 @@ class DockerHelperTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 USER my-user
                 RUN apt-get update -y && apt-get install -y nano
                 '''.stripIndent()
@@ -315,6 +321,7 @@ class DockerHelperTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 USER my-user
                 RUN apt-get update -y && apt-get install -y procps
                 '''.stripIndent()