Fix broken Docker image

NBISweden · Nov 13, 2024 · 1682dd0 · 1682dd0
1 parent d17a01a
commit 1682dd0
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/tutorials/containers/Dockerfile b/tutorials/containers/Dockerfile
@@ -25,9 +25,12 @@ RUN conda config --set channel_priority strict && \
 
 # Install environment
 COPY environment.yml ./
-RUN conda env update -f environment.yml -n base && \
+RUN conda env create -f environment.yml -n project_mrsa && \
     conda clean -a
 
+RUN echo "source activate project_mrsa" >> ~/.bashrc
+ENV PATH /opt/conda/envs/project_mrsa/bin:${PATH}
+
 # Add project files
 COPY Snakefile config.yml ./
 COPY code ./code/

diff --git a/tutorials/containers/environment.yml b/tutorials/containers/environment.yml
@@ -11,7 +11,7 @@ dependencies:
   - bowtie2
   - tbb
   - samtools
-  - subread
+  - subread>=2
   - bedtools
   - r-base
   - r-ggplot2