Add procps to Conda-based container builds

Signed-off-by: Paolo Di Tommaso <[email protected]>
seqeralabs · Sep 21, 2023 · 2537882 · 2537882
1 parent f26d7b8
commit 2537882
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Showing 2 changed files with 18 additions and 12 deletions.
diff --git a/app/build.gradle b/app/build.gradle
@@ -21,7 +21,7 @@ repositories {
 
 dependencies {
     implementation 'io.seqera:wave-api:0.5.0'
-    implementation 'io.seqera:wave-utils:0.7.4'
+    implementation 'io.seqera:wave-utils:0.7.5'
     implementation 'info.picocli:picocli:4.6.1'
     implementation 'com.squareup.moshi:moshi:1.14.0'
     implementation 'com.squareup.moshi:moshi-adapters:1.14.0'

diff --git a/app/src/test/groovy/io/seqera/wavelit/AppCondaOptsTest.groovy b/app/src/test/groovy/io/seqera/wavelit/AppCondaOptsTest.groovy
@@ -113,6 +113,7 @@ class AppCondaOptsTest extends Specification {
                 FROM mambaorg/micromamba:1.4.9
                 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 clean -a -y
                 USER root
                 '''.stripIndent()
@@ -138,6 +139,7 @@ class AppCondaOptsTest extends Specification {
                 FROM mambaorg/micromamba:1.4.9
                 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 clean -a -y
                 USER root
                 '''.stripIndent()
@@ -166,8 +168,8 @@ class AppCondaOptsTest extends Specification {
         new String(req.containerFile.decodeBase64()) == '''\
                 FROM mambaorg/micromamba:1.4.9
                 RUN \\
-                    micromamba install -y -n base -c seqera -c bioconda -c conda-forge -c defaults \\
-                    -f https://host.com/file-lock.yml \\
+                    micromamba install -y -n base -c seqera -c bioconda -c conda-forge -c defaults -f https://host.com/file-lock.yml \\
+                    && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
                 '''.stripIndent()
@@ -197,6 +199,7 @@ class AppCondaOptsTest extends Specification {
                 FROM my/mamba:latest
                 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 clean -a -y
                 USER root
                 RUN one
@@ -235,8 +238,9 @@ class AppCondaOptsTest extends Specification {
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
-                    micromamba install -y -n base -f /scratch/conda.yml \\
-                    && micromamba clean -a -y
+                    micromamba install -y -n base -f /scratch/conda.yml
+                    micromamba install -y -n base conda-forge::procps-ng
+                    micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
@@ -264,8 +268,9 @@ class AppCondaOptsTest extends Specification {
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
-                    micromamba install -y -n base -f /scratch/conda.yml \\
-                    && micromamba clean -a -y
+                    micromamba install -y -n base -f /scratch/conda.yml
+                    micromamba install -y -n base conda-forge::procps-ng
+                    micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()
@@ -305,8 +310,9 @@ class AppCondaOptsTest extends Specification {
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
-                    micromamba install -y -n base -f /scratch/conda.yml \\
-                    && micromamba clean -a -y
+                    micromamba install -y -n base -f /scratch/conda.yml
+                    micromamba install -y -n base conda-forge::procps-ng
+                    micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 %post
@@ -339,9 +345,9 @@ class AppCondaOptsTest extends Specification {
             BootStrap: docker
             From: mambaorg/micromamba:1.4.9
             %post
-                micromamba install -y -n base -c seqera -c bioconda -c conda-forge -c defaults \\
-                -f https://host.com/file-lock.yml \\
-                && micromamba clean -a -y
+                micromamba install -y -n base -c seqera -c bioconda -c conda-forge -c defaults -f https://host.com/file-lock.yml
+                micromamba install -y -n base conda-forge::procps-ng
+                micromamba clean -a -y
             %environment
                 export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                 '''.stripIndent()