From b22d17090b778469ebf38c8168a08fd6578a661c Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Sat, 15 Mar 2014 22:08:58 +0100
Subject: [PATCH] The installing lecture now uses pframes.
---
installing/installing.tex | 96 ++++++++++++++++-----------------------
1 file changed, 39 insertions(+), 57 deletions(-)
diff --git a/installing/installing.tex b/installing/installing.tex
index 1a40e5f..8080980 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}
--
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