diff --git a/connecting/connecting.tex b/connecting/connecting.tex
index 0a0bf866c9ffe0693d0195b5a7f0eee3fb925932..bc634141bfe08b0332c8cb1664c82161403d25af 100644
--- a/connecting/connecting.tex
+++ b/connecting/connecting.tex
@@ -30,9 +30,8 @@
% First page of the presentation.
\section{Introdution}
-\begin{frame}
- \frametitle{Servers}
-
+\subsection{Servers}
+\begin{pframe}
Remote machines can be very convenient:
\begin{itemize}
\item One central machine for calculation.
@@ -42,23 +41,22 @@
\item Multiple users can use it at the same time.
\item \ldots
\end{itemize}
-\end{frame}
+\end{pframe}
\section{Using servers}
-\begin{frame}
- \frametitle{Logging in}
-
+\subsection{Logging in}
+\begin{pframe}
There are lots of ways to connect to a server.
\begin{itemize}
\item HTTP -- When visiting websites.
\item IMAP -- When fetching mail.
\item \ldots
\end{itemize}
- \bigskip
+ \medskip
\pause
In order to execute commands, we need to \emph{log in}.
- \bigskip
+ \medskip
We use a \emph{secure} protocol to log in.
\begin{itemize}
@@ -66,15 +64,13 @@
\item When working with patient data, we don't want eavesdropping.
\item The connection from your machine to the server is \emph{encrypted}.
\end{itemize}
-\end{frame}
-
-\begin{frame}[fragile]
- \frametitle{Secure Shell}
+\end{pframe}
+\subsection{Secure Shell}
+\begin{pframe}
\begin{lstlisting}[language=none, caption=Using Secure Shell (ssh)..]
$ ssh user@host
\end{lstlisting}
- \bigskip
\begin{table}[]
\begin{center}
@@ -93,12 +89,11 @@
\begin{lstlisting}[language=none, caption=Example.]
$ ssh course@shark
\end{lstlisting}
-\end{frame}
+\end{pframe}
\section{File transfer}
-\begin{frame}
- \frametitle{Copying data}
-
+\subsection{Copying data}
+\begin{pframe}
We frequently need to transfer data before and after we do an analysis.
\begin{itemize}
\item The input needs to be on the server.
@@ -116,15 +111,13 @@
\item Copy data from the server to your machine (downloading).
\end{itemize}
\end{itemize}
-\end{frame}
-
-\begin{frame}[fragile]
- \frametitle{Secure Copy}
+\end{pframe}
+\subsection{Secure Copy}
+\begin{pframe}
\begin{lstlisting}[language=none, caption=Copying something to the server.]
$ scp localfile user@host:/path/to/remotefile
\end{lstlisting}
- \bigskip
\begin{table}[]
\begin{center}
@@ -139,18 +132,17 @@
\bt{remotefile} & Name of the file on the \emph{server}.
\end{tabular}
\end{center}
- \caption{}
+ \caption{Description of the parameters.}
\label{}
\end{table}
-\end{frame}
-
-\begin{frame}[fragile]
- \frametitle{Secure Copy}
+\end{pframe}
+\begin{pframe}
\begin{lstlisting}[language=none, caption=Example.]
$ scp localfile host:
$ scp host:remotefile .
\end{lstlisting}
+ \vspace{-0.5cm}
\begin{table}[]
\begin{center}
@@ -168,12 +160,11 @@
\caption{Some defaults (when left empty).}
\label{}
\end{table}
-\end{frame}
+\end{pframe}
\section{Connecting from an other OS}
-\begin{fframe}
- \frametitle{Windows}
-
+\subsection{Windows}
+\begin{pframe}
Windows does not have the \bt{ssh} command, but there are programs that
give the same functionality.
\bigskip
@@ -189,12 +180,10 @@
\end{itemize}
\vfill
- \bs{http://www.chiark.greenend.org.uk/~sgtatham/putty}
-\end{fframe}
-
-\begin{frame}
- \frametitle{Windows}
+ \permfoot{http://www.chiark.greenend.org.uk/~sgtatham/putty}
+\end{pframe}
+\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.8\textheight]{PuTTY_login}
@@ -202,11 +191,9 @@
\caption{Connecting to a server using PuTTY.}
\label{}
\end{figure}
-\end{frame}
-
-\begin{frame}
- \frametitle{Windows}
+\end{pframe}
+\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.8\textheight]{PuTTY_terminal}
@@ -214,12 +201,11 @@
\caption{A terminal when connected to a server.}
\label{}
\end{figure}
-\end{frame}
+\end{pframe}
\section{Examples}
-\begin{frame}
- \frametitle{Typical workflow}
-
+\subsection{Typical workflow}
+\begin{pframe}
When doing an analysis, the general workflow looks like this:
\begin{itemize}
\item First copy the input data to the server.
@@ -229,16 +215,14 @@
\item Clean up the input data and the results on the server.
\item Log out.
\end{itemize}
-\end{frame}
-
-\begin{frame}[fragile]
- \frametitle{Typical workflow: an example}
+\end{pframe}
+\subsection{Typical workflow: an example}
+\begin{pframe}
Step one: preparing the input.
\bigskip
On your machine, copy the raw data to the server, then log in on the server.
- \bigskip
\begin{lstlisting}[language=none, caption=Copy data to the server and log
in.]
@@ -248,16 +232,13 @@
\bigskip
Now the file \bt{reads.fq} is available on the server.
-\end{frame}
-
-\begin{frame}[fragile]
- \frametitle{Typical workflow: an example}
+\end{pframe}
+\begin{pframe}
Step two: The analysis.
\bigskip
On the server, you can do an analysis.
- \bigskip
\begin{lstlisting}[language=none, caption=Example pipeline.]
$ bwa aln ./indexes/chr17.fa reads.fq > reads.sai
@@ -269,40 +250,34 @@
$ samtools pileup -vcf ./indexes/chr17.fa \
reads.bam.sorted.bam > reads.pileup
\end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
- \frametitle{Typical workflow: an example}
+\end{pframe}
+\begin{pframe}
Step three: Retrieving the output.
\bigskip
Copy the output from the server back to your own machine.
- \bigskip
\begin{lstlisting}[language=none, caption=Copy data from the server.]
$ scp course@shark:reads.pileup .
\end{lstlisting}
- \bigskip
\pause
Step four: Cleaning up.
\bigskip
Clean up on the server and leave.
- \bigskip
\begin{lstlisting}[language=none, caption=Delete temporary files and log
out.]
$ rm reads.*
$ logout
\end{lstlisting}
-\end{frame}
+\end{pframe}
\section{Why remote servers?}
-\begin{fframe}
- \frametitle{Clusters}
-
+\subsection{Clusters}
+\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.8\textheight]{supercomputer}
@@ -313,11 +288,9 @@
\vfill
\permfoot{http://en.wikipedia.org/wiki/IBM\_Roadrunner}
-\end{fframe}
-
-\begin{frame}
- \frametitle{Clusters}
+\end{pframe}
+\begin{pframe}
Massive parallel computing.
\begin{itemize}
\item A large number of computers working together.
@@ -337,11 +310,9 @@
\item Chop the problem op in parts / combine the results.
\end{itemize}
\end{itemize}
-\end{frame}
-
-\begin{frame}
- \frametitle{Clusters}
+\end{pframe}
+\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.8\textheight]{cluster-schematic}
@@ -349,11 +320,9 @@
\caption{Schematic overview of a cluster.}
\label{}
\end{figure}
-\end{frame}
-
-\begin{frame}
- \frametitle{Clusters}
+\end{pframe}
+\begin{pframe}
General characteristics of a cluster.
\begin{itemize}
\item Jobs are submitted to a \emph{control node}.
@@ -368,11 +337,11 @@
\item Jobs can be prioritised.
\item \ldots
\end{itemize}
-\end{frame}
+\end{pframe}
\section{Questions?}
\lastpagetemplate
-\begin{fframe}
+\begin{pframe}
\begin{center}
\bigskip
\bigskip
@@ -386,5 +355,5 @@
\vfill
\permfoot{https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/NGS-intro}
-\end{fframe}
+\end{pframe}
\end{document}