The installing lecture now uses pframes.

installing/installing.tex

@@ -31,9 +31,8 @@
 
 % First page of the presentation.
 \section{Simple installation}
-\begin{frame}[fragile]
-  \frametitle{Updating.}
-
+\subsection{Updating.}
+\begin{pframe}
   First of all, run the update command to make sure we download the latest
   versions.
   \bigskip
@@ -51,11 +50,10 @@
   \begin{lstlisting}[language=none, caption=Upgrade to the newest version.]
     $ sudo apt-get upgrade
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Small packages.}
+\end{pframe}
 
+\subsection{Small packages.}
+\begin{pframe}
   In many cases, the package name is equal to the command we want to use:
   \bigskip
 
@@ -66,11 +64,10 @@
     $ sudo apt-get install sl
     $ sl
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Searching for packages.}
+\end{pframe}
 
+\subsection{Searching for packages.}
+\begin{pframe}
   If we want to search for all packages that have anything to do with
   ``alignment'':
   \bigskip
@@ -88,11 +85,10 @@
                   DNA and protein sequences
     ...
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Searching package content.}
+\end{pframe}
 
+\subsection{Searching package content.}
+\begin{pframe}
   Suppose we know a command, but we do not know which package to install:
   \bigskip
 
@@ -102,11 +98,9 @@
   \bigskip
 
   This will return nothing (unlike our ``\bt{sl}'' example).
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Searching package content.}
+\end{pframe}
 
+\begin{pframe}
   Get a list of packages that provide the file ``\bt{exonerate}''.
   \bigskip
 
@@ -124,12 +118,11 @@
   \begin{lstlisting}[language=none, caption=Install the right package.]
     $ sudo apt-get install exonerate
   \end{lstlisting}
-\end{frame}
+\end{pframe}
 
 \section{Manual installation}
-\begin{frame}
-  \frametitle{Why manual installation?}
-
+\subsection{Why manual installation?}
+\begin{pframe}
   Reasons for manual installation:
   \begin{itemize}
     \item There is no package available.
@@ -144,25 +137,23 @@
     \item Download an \emph{archive} from the internet.
     \item Extract the content.
   \end{itemize}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Archives.}
+\end{pframe}
 
+\subsection{Archives.}
+\begin{pframe}
   Commonly used archiving programs:
   \begin{itemize}
     \item \bt{tar} in combination with \bt{gzip} or \bt{bzip2}.
     \item \bt{zip}.
   \end{itemize}
-  \bigskip
+  \medskip
 
   Zip is commonly used for Windows and is easy to use for Linux.
-  \bigskip
 
   \begin{lstlisting}[language=none, caption=Unpack a zip archive.]
     $ unzip archivename.zip
   \end{lstlisting}
-  \bigskip
+  \medskip
   \pause
 
   \begin{lstlisting}[language=none, caption=Create a zip archive.]
@@ -170,11 +161,9 @@
   \end{lstlisting}
 
   The option \bt{-r} stands for \emph{recursive}.
-\end{frame}
-
-\begin{frame}
-  \frametitle{Archives.}
+\end{pframe}
 
+\begin{pframe}
   Tar is an old program used to pack lots of files into one archive to put it
   on tape (hence the name Tape ARchive).
   \bigskip
@@ -201,11 +190,9 @@
     \caption{Extensions of compressed tar archives.}
     \label{}
   \end{table}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Archives.}
+\end{pframe}
 
+\begin{pframe}
   Commonly used options for \bt{tar}:
   \bigskip
 
@@ -225,11 +212,10 @@
     \caption{Commonly used Tar options.}
     \label{}
   \end{table}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Example extraction.}
+\end{pframe}
 
+\subsection{Example extraction.}
+\begin{pframe}
   Extraction of a \bt{tar.gz} file (\bt{tar} compressed with \bt{gzip}):
   \bigskip
 
@@ -245,11 +231,9 @@
   \begin{lstlisting}[language=none, caption=Create a compressed archive.]
     $ tar -czvf myarchive.tar.gz directoryname
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Example extraction.}
+\end{pframe}
 
+\begin{pframe}
   Extraction of a \bt{tar.bz2} file (\bt{tar} compressed with \bt{bzip2}):
   \bigskip
 
@@ -265,11 +249,10 @@
   \begin{lstlisting}[language=none, caption=Create a compressed archive.]
     $ tar -cjvf myarchive.tar.bz2 directoryname
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Installing software: Manual installation}
+\end{pframe}
 
+\subsection{Installing software: Manual installation}
+\begin{pframe}
   If there are no \emph{executables} available, we have to make them ourselves.
   \begin{itemize}
     \item Go to the Bowtie website.
@@ -287,12 +270,11 @@
     $ make
     $ ./bowtie -h
   \end{lstlisting}
-\end{frame}
+\end{pframe}
 
 \section{Practical session}
-\begin{frame}
-  \frametitle{About this part of the course}
-
+\subsection{About this part of the course}
+\begin{pframe}
   \bigskip
   \bigskip
   \begin{itemize}
@@ -303,11 +285,11 @@
     \item We are going to connect to other machines (servers that have more
       memory or computing power).
   \end{itemize}
-\end{frame}
+\end{pframe}
 
 \section{Questions?}
 \lastpagetemplate
-\begin{fframe}
+\begin{pframe}
   \begin{center}
     \bigskip
     \bigskip
@@ -321,5 +303,5 @@
 
   \vfill
   \permfoot{https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/NGS-intro}
-\end{fframe}
+\end{pframe}
 \end{document}