Finished practical 2

practical_two/practical_two.tex

@@ -32,35 +32,103 @@
 
 % Pipeline
 \section{A simple analysis pipeline}
-Log in to the virtual machine as described in the first practical. Finish the
-other pratical first then continue with this one.
+Log in to the virtual machine as described in the first practical. Finish these
+exercises first then continue with this one.
 \bigskip
 
-An anlysis pipelines vary from a couple of very simple lines of code, to
-complex frameworks. The idea behind it is always the same. Make your analysis
-easier. At the same time, your analysis becomes reproducable, documented and
-easier to share.
+Anlysis pipelines can vary from a couple of very simple lines of code, to
+complex frameworks working on multiple computing nodes. However, the idea
+behind it is always the same. Make your analysis easier, while at the same time
+it becomes reproducable, documented and easier to share.
 \medskip
 
-Today we will use bash to create a basic pipeline. 
+Today we will use bash to create a basic pipeline. Unknowingly, you have
+already worked with bash. Everything you've typed into the terminal so far is
+basically part of bash. To create a pipeline, all we need to do is create a
+file with the ``.sh'' extension and simply sum up the steps you want to include.
+\medskip
+
+First, let's see how to make your script executable. We need to change the
+permissions. This way you can simply run the file directly without having to
+specify the interpreter. In Linux we us chmod for this.
+\medskip
+
+\begin{lstlisting}
+  $ chmod +x file.sh
+\end{lstlisting}
+\medskip
+
+One last additional piece of information your system is missing, is which
+interpertaor it should use. We store this in the very first line of the script
+and is written like this ``\#!/bin/bash''.
+\medskip
+
+This is all you need to know to write your first pipeline. Bash offers a lot
+more possibilities than just using Linux powertools, navigation and starting
+other software. For example, to make the pipeline easier to re-use with other
+data, we can give a bash script parameters. Just like Bowtie, where you can
+supply your fastq file. This is done by using the reserved variable \$1 inside
+the script. Everywhere in your script this variable will be replace with the
+first argument you give on the command line.
+\medskip
+
+The next exercise will give you an idea on how to structure a simple bash
+pipeline. Complete the exercise and try to understand what is going on in the 
+script:
 \medskip
 
-Write a short bash pipeline that:
 \begin{itemize}
-  \item Aligns a given fastq file to the mtDNA
-  \item Has comments to explain what happens
-  \item Is executable
+  \item Write the lines you see below to a file ``Hello.sh''
+  \item Make the file executable ``chmod +x Hello.sh''
+  \item Run it with an argument ``./Hello.sh yourname'' and see what it does
+  \item Comments start with \# and are used to document your work
 \end{itemize}
 \medskip
 
-Hints:
+\begin{lstlisting}
+  #!/bin/bash
+  echo Hello \$1, the date is:
+  # The next line will print the date.
+  date
+\end{lstlisting}
+\medskip
+
+With this knowledge you should be able to write your own short bash pipeline.
+Combine this with what you have learned in the first practical and try to write
+a script that combines the tools from the first practical into a pipeline:
+\medskip
+
+\begin{itemize}
+  \item Inlcude these steps:
+  \begin{itemize}
+    \item Align a fastq file to the mtDNA
+    \item Convert the SAM to a sorted BAM
+    \item Call variants
+    \item Annotate the variants
+  \end{itemize}
+  \item Keep these things in mind when writing the script:
+  \begin{itemize}
+    \item The fastq file should be the first argument
+    \item Use comments to explain what happens
+    \item Make it executable
+    \item Bonus: Can you think of adding more arguments? Maybe for annotation?
+  \end{itemize}
+\end{itemize}
+\medskip
+
+Hints and summary:
 \begin{itemize}
   \item A comment line starts with an \#
-  \item \$1 is the first argument
-  \item Make your pipeline executable with ``chmod +x''
+  \item \$1 is the first argument, \$2 the second, etc...
+  \item Make your pipeline executable with ``chmod +x file''
 \end{itemize}
 \medskip
 
-This is the end of the practical. Now you know how to write a basic pipeline.
-Thanks for participating! 
+Now you know how to write a basic pipeline. In bash you can also work with
+conditions, loops and error handling but this is beyond the scope of this
+course. If you like to know more there is plenty to read on the web or visit
+one of our other courses. This is the end of the practical.
+\medskip
+
+Thank you for participating! 
 \end{document}