Specify bash code chunks

README.Rmd

@@ -49,7 +49,7 @@ the JASPAR or the provided database.
 [`memes`](https://www.bioconductor.org/packages/release/bioc/html/memes.html)
 which relies on a local install of the
 [MEME suite](https://meme-suite.org/meme/), which can be installed as follows:
-```
+```bash
 MEME_VERSION=5.5.5  # or the latest version
 
 wget https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz
@@ -68,7 +68,7 @@ source ~/.bashrc
 **NOTE:** It is important that Perl dependencies associated with MEME suite are
 also installed, particularly `XML::Parser`, which can be installed using the
 following command in the terminal:
-```
+```bash
 cpan install XML::Parser
 ```
 For more information, refer to the [Perl dependency section of the MEME suite](https://meme-suite.org/meme/doc/install.html#prereq_perl).

README.md

@@ -50,25 +50,29 @@ package outputs an HTML report consisting of three sections:
 which relies on a local install of the [MEME
 suite](https://meme-suite.org/meme/), which can be installed as follows:
 
-    MEME_VERSION=5.5.5  # or the latest version
-
-    wget https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz
-    tar zxf meme-$MEME_VERSION.tar.gz
-    cd meme-$MEME_VERSION
-    ./configure --prefix=$HOME/meme --with-url=http://meme-suite.org/ \
-    --enable-build-libxml2 --enable-build-libxslt
-    make
-    make install
-
-    # Add to PATH
-    echo 'export PATH=$HOME/meme/bin:/meme/libexec/meme-$MEME_VERSION:$PATH' >> ~/.bashrc
-    source ~/.bashrc
+``` bash
+MEME_VERSION=5.5.5  # or the latest version
+
+wget https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz
+tar zxf meme-$MEME_VERSION.tar.gz
+cd meme-$MEME_VERSION
+./configure --prefix=$HOME/meme --with-url=http://meme-suite.org/ \
+--enable-build-libxml2 --enable-build-libxslt
+make
+make install
+
+# Add to PATH
+echo 'export PATH=$HOME/meme/bin:/meme/libexec/meme-$MEME_VERSION:$PATH' >> ~/.bashrc
+source ~/.bashrc
+```
 
 **NOTE:** It is important that Perl dependencies associated with MEME
 suite are also installed, particularly `XML::Parser`, which can be
 installed using the following command in the terminal:
 
-    cpan install XML::Parser
+``` bash
+cpan install XML::Parser
+```
 
 For more information, refer to the [Perl dependency section of the MEME
 suite](https://meme-suite.org/meme/doc/install.html#prereq_perl).

vignettes/MotifPeeker.Rmd

@@ -75,7 +75,7 @@ package.
 [`memes`](https://www.bioconductor.org/packages/release/bioc/html/memes.html)
 which relies on a local install of the
 [MEME suite](https://meme-suite.org/meme/), which can be installed as follows:
-```
+```bash
 MEME_VERSION=5.5.5  # or the latest version
 
 wget https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz
@@ -94,7 +94,7 @@ source ~/.bashrc
 **NOTE:** It is important that Perl dependencies associated with MEME suite are
 also installed, particularly `XML::Parser`, which can be installed using the
 following command in the terminal:
-```
+```bash
 cpan install XML::Parser
 ```
 For more information, refer to the [Perl dependency section of the MEME suite](https://meme-suite.org/meme/doc/install.html#prereq_perl).

vignettes/troubleshooting.Rmd

@@ -29,7 +29,7 @@ If you encounter an issue that is not covered, please open an issue on the
    [Perl dependencies required by the MEME Suite](https://meme-suite.org/meme/doc/install.html#prereq_perl)
    are installed, particularly `XML::Parser`, which can be installed using the
    following command in the terminal:  
-   ```
+   ```bash
    cpan install XML::Parser
    ```
 
@@ -41,3 +41,16 @@ If you encounter an issue that is not covered, please open an issue on the
   running the `MotifPeeker()` function.  
   Additionally, follow the [runtime guidance](https://neurogenomics.github.io/MotifPeeker/articles/MotifPeeker.html#runtime)
   for `MotifPeeker()`.  
+
+
+# Session Info 
+
+<details> 
+
+```{r session-info}
+utils::sessionInfo()
+```
+
+</details>  
+
+<br>