Use root user in Wave container based on micromamba (#4038) [ci fast]

Signed-off-by: Marco De La Pierre <[email protected]>
nextflow-io · Aug 15, 2023 · a3a75ea · a3a75ea
1 parent 552501c
commit a3a75ea
Show file tree

Hide file tree

Showing 4 changed files with 11 additions and 0 deletions.
diff --git a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt b/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt
@@ -3,3 +3,4 @@ COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
 RUN micromamba install -y -n base -f /tmp/conda.yml \
     {{base_packages}}
     && micromamba clean -a -y
+USER root
diff --git a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt b/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt
@@ -4,3 +4,4 @@ RUN \
     {{target}} \
     {{base_packages}}
     && micromamba clean -a -y
+USER root
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -476,6 +476,7 @@ class WaveClientTest extends Specification {
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     salmon=1.2.3 \\
                     && micromamba clean -a -y
+                USER root
                     '''.stripIndent()
         and:
         !assets.moduleResources
@@ -544,6 +545,7 @@ class WaveClientTest extends Specification {
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba clean -a -y
+                USER root
                     '''.stripIndent()
         and:
         assets.condaFile == condaFile

diff --git a/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
@@ -41,6 +41,7 @@ class DockerHelperTest extends Specification {
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -52,6 +53,7 @@ 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 clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -67,6 +69,7 @@ class DockerHelperTest extends Specification {
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     bwa=0.7.15 salmon=1.1.1 \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -84,6 +87,7 @@ class DockerHelperTest extends Specification {
                     bwa=0.7.15 salmon=1.1.1 \\
                     && micromamba install -y -n base foo::one bar::two \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -99,6 +103,7 @@ class DockerHelperTest extends Specification {
                     micromamba install -y -n base -c foo -c bar \\
                     bwa=0.7.15 salmon=1.1.1 \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -115,6 +120,7 @@ class DockerHelperTest extends Specification {
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     bwa=0.7.15 salmon=1.1.1 \\
                     && micromamba clean -a -y
+                USER root
                 USER my-user
                 RUN apt-get update -y && apt-get install -y nano
                 '''.stripIndent()
@@ -134,6 +140,7 @@ class DockerHelperTest extends Specification {
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     -f https://foo.com/some/conda-lock.yml \\
                     && micromamba clean -a -y
+                USER root
                 USER my-user
                 RUN apt-get update -y && apt-get install -y procps
                 '''.stripIndent()