fixing codeblocks

coderefinery · Apr 6, 2024 · cc6f2ff · cc6f2ff
1 parent ea08e67
commit cc6f2ff
Showing 1 changed file with 7 additions and 8 deletions.
diff --git a/content/advanced_recipe.rst b/content/advanced_recipe.rst
@@ -19,7 +19,7 @@ Building a scientific software stack in a container can be challenging due to de
 
 First, we'll outline a container recipe that includes a typical setup for a bioinformatics analysis environment, featuring tools like BLAST, Python, and R.
 
-   ``` bash
+.. code-block:: bash
    # Example Apptainer definition file for a bioinformatics stack
    Bootstrap: library
    From: ubuntu:20.04
@@ -38,21 +38,20 @@ First, we'll outline a container recipe that includes a typical setup for a bioi
        echo "Environment for bioinformatics analysis ready. Tools available: BLAST, Python, R."
        exec /bin/bash
    
-   ```
 
-   ``` bash
+.. code-block:: bash
    # Build the container for the bioinformatics stack
    apptainer build bioinfo_container.sif bioinfo.def
-   ```
 
-This block constructs the `bioinfo_container.sif` from the `bioinfo.def` file. It installs critical tools for bioinformatics, including BLAST for sequence analysis, and a suite of Python and R libraries commonly used in data analysis and visualization.
 
-   ``` bash
+This block constructs the ``bioinfo_container.sif`` from the ``bioinfo.def`` file. It installs critical tools for bioinformatics, including BLAST for sequence analysis, and a suite of Python and R libraries commonly used in data analysis and visualization.
+
+.. code-block:: bash
    # Run the container, providing an interactive shell
    apptainer shell bioinfo_container.sif
-   ```
 
-This command provides an interactive shell within the `bioinfo_container.sif`, allowing users to execute the installed tools and perform analyses as if they were running on a native environment. This setup is ideal for ensuring that all users, regardless of their host system configuration, can reproduce the scientific computations.
+
+This command provides an interactive shell within the ``bioinfo_container.sif``, allowing users to execute the installed tools and perform analyses as if they were running on a native environment. This setup is ideal for ensuring that all users, regardless of their host system configuration, can reproduce the scientific computations.
 
 Summary
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