diff --git a/installing/installing.tex b/installing/installing.tex index 1a40e5f287f4c7393cdb2b8817cb0e3cce24c230..80809802cb1c571b3a8b8ecce9c9a24625440c3d 100644 --- a/installing/installing.tex +++ b/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}