add conda to env to run commands not set for exec

karlnyr · karlnyr · commit 4abf6fcaee0d · 2026-03-12T10:57:24.000+01:00
diff --git a/containers/Dockerfile.blast b/containers/Dockerfile.blast
@@ -15,3 +15,5 @@ USER $MAMBA_USER
 RUN micromamba install -y -n base -c conda-forge -c bioconda \
         blast=2.12.0 \
     && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"
diff --git a/containers/Dockerfile.bwa b/containers/Dockerfile.bwa
@@ -15,3 +15,5 @@ USER $MAMBA_USER
 RUN micromamba install -y -n base -c conda-forge -c bioconda \
         bwa=0.7.17 \
     && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"
diff --git a/containers/Dockerfile.picard b/containers/Dockerfile.picard
@@ -19,3 +19,5 @@ RUN micromamba install -y -n base -c conda-forge -c bioconda \
         picard=2.20.3 \
         r-base=4.1.1 \
     && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"
diff --git a/containers/Dockerfile.quast b/containers/Dockerfile.quast
@@ -17,3 +17,5 @@ USER $MAMBA_USER
 RUN micromamba install -y -n base -c conda-forge -c bioconda \
         quast=5.3.0 \
     && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"
diff --git a/containers/Dockerfile.samtools b/containers/Dockerfile.samtools
@@ -15,3 +15,5 @@ USER $MAMBA_USER
 RUN micromamba install -y -n base -c conda-forge -c bioconda \
         samtools=1.13 \
     && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"
diff --git a/containers/Dockerfile.skesa b/containers/Dockerfile.skesa
@@ -15,3 +15,5 @@ USER $MAMBA_USER
 RUN micromamba install -y -n base -c conda-forge -c bioconda \
         skesa=2.5.1 \
     && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"
diff --git a/containers/Dockerfile.trimmomatic b/containers/Dockerfile.trimmomatic
@@ -19,3 +19,5 @@ USER $MAMBA_USER
 RUN micromamba install -y -n base -c conda-forge -c bioconda \
         trimmomatic=0.39 \
     && micromamba clean -afy
+
+ENV PATH="/opt/conda/bin:$PATH"
