Added packages slides.

lectures/packages/Makefile

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lectures/packages/beamerthemelumc.sty

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lectures/packages/gen2phen_logo.eps

+../../submodules/presentation/gen2phen_logo.eps
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lectures/packages/lgtc_logo.eps

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lectures/packages/lumc_logo.eps

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lectures/packages/lumc_logo_small.eps

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lectures/packages/nbic_logo.eps

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lectures/packages/ngi_logo.eps

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lectures/packages/packages.tex

+\documentclass[slidestop]{beamer}
+
+\title{Python Packages of Popular Programs}
+\providecommand{\myConference}{Work discussion}
+\providecommand{\myDate}{Wednesday, 8 May 2013}
+\author{Jeroen F. J. Laros}
+\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\lastCenterLogo}{
+  \raisebox{-0.1cm}{
+    \includegraphics[height = 1cm]{lgtc_logo}
+    %\includegraphics[height = 0.7cm]{ngi_logo}
+  }
+}
+\providecommand{\lastRightLogo}{
+  %\includegraphics[height = 0.7cm]{nbic_logo}
+  %\includegraphics[height = 0.8cm]{nwo_logo_en}
+  %\hspace{1.5cm}\includegraphics[height = 0.7cm]{gen2phen_logo}
+}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title page.
+\bodytemplate
+
+% First page of the presentation.
+\section{Introduction}
+\begin{frame}[fragile]
+  \frametitle{Distributing programs}
+
+  Via PyPI - the Python Package Index.
+  \bigskip
+
+  \begin{itemize}
+    \item Anyone can install your software easily.
+    \item Dependencies are automatically installed.
+    \item No more sharing of scripts.
+    \begin{itemize}
+      \item \ldots that need the help of the developer to run.
+    \end{itemize}
+  \end{itemize}
+  \bigskip
+  \bigskip
+  \pause
+
+  \begin{lstlisting}[language=bash]
+    pip install tssv
+  \end{lstlisting}
+\end{frame}
+
+%\begin{frame}
+%  \frametitle{The problem with scripts.}
+%\end{frame}
+%
+%\begin{frame}
+%  \frametitle{Solution for source.}
+%\end{frame}
+%
+%\begin{frame}
+%  \frametitle{The problem with distributing source.}
+%\end{frame}
+%
+%\section{Packages}
+%\begin{frame}
+%  \frametitle{Professional distribution.}
+%
+%  Make things so easy for the end-user that they will not share programs.
+%\end{frame}
+
+\section{LUMC packages}
+\begin{fframe}
+  \frametitle{Released packages}
+
+  We currently have released the following packages:
+  \begin{itemize}
+    \item wiggelen
+    \item fastools
+    \item piletools
+    \item barcode
+    \item tssv
+    \item kMer
+  \end{itemize}
+
+  \vfill
+  \permfoot{https://pypi.python.org/}
+\end{fframe}
+
+\begin{fframe}
+  \frametitle{wiggelen}
+
+  Working with wiggle tracks in Python.
+
+  \begin{table}[]
+    \begin{center}
+      \begin{tabular}{lp{7cm}}
+        command         & explanation\\
+        \hline
+        \bt{index}      & build index for wiggle track\\
+        \bt{sort}       & sort wiggle track regions alphabetically\\
+        \bt{scale}      & scale values in a wiggle track\\
+        \bt{merge}      & merge wiggle tracks in various ways\\
+        \bt{distance}   & calculate distances between tracks\\
+        \bt{coverage}   & convert a track to coverage intervals\\
+        \bt{derivative} & create derivative of a wiggle track
+      \end{tabular}
+    \end{center}
+    \caption{Functionality of \bt{wiggelen}.}
+    \label{}
+  \end{table}
+
+  \vfill
+  Obsoletes: \bs{wiggledist}, \bs{wigglemerge}, \bs{wiggle2region}.
+\end{fframe}
+
+\begin{fframe}
+  \frametitle{piletools}
+
+  Toolkit for the analysis of pileup files (depends on \bt{wiggelen}).
+
+  \begin{table}[]
+    \begin{center}
+      \begin{tabular}{lp{7cm}}
+        command             & explanation\\
+        \hline
+        \bt{mpileup2wig}    & convert an mpileup file to to a wiggle file\\
+        \bt{mpileup2tagwig} & record 5' or 3' ends of reads, strand specific
+      \end{tabular}
+    \end{center}
+    \caption{Functionality of \bt{piletools}.}
+    \label{}
+  \end{table}
+
+  \vfill
+  Obsoletes: \bs{mpileup2wig}, \bs{sageWiggle}.
+\end{fframe}
+
+\begin{fframe}
+  \frametitle{fastools}
+
+  Toolkit for the analysis and manipulation of FASTA/Q files.
+
+  \begin{table}[]
+    \begin{center}
+      \begin{tabular}{ll}
+        command  & explanation\\
+        \hline
+        sanitise & convert to standard FASTA/FASTQ\\
+        add      & add a '5 sequence\\
+        select   & select a part of every sequence\\
+        get      & retrieve a sequence from the NCBI\\
+        lenfilt  & split a FASTA/FASTQ file based on length
+      \end{tabular}
+    \end{center}
+    \caption{Highlights of \bt{fastools}.}
+    \label{}
+  \end{table}
+
+  \vfill
+  Obsoletes: \bs{fa2fa}, \bs{fa2fq}, \bs{fq2fa},
+    \bs{GAPSS\_add\_5prime\_sequence\_v2\_Sanger}, \bs{alignRefSeqs},
+    \bs{restrict}, \bs{collapse}, \bs{sanger2illumina}, \bs{select},
+    \bs{fa2gb}, \bs{gb2fa}, \bs{fastaMangle}, \bs{generateDNA},
+    \bs{getReference}, \bs{lengthFilter}, \bs{ngslib}
+\end{fframe}
+
+\begin{fframe}
+  \frametitle{fastools}
+
+  Also includes a demultiplexer.
+
+  \begin{itemize}
+    \item Allows for mismatches (default $1$).
+    \item Guess barcodes (supply amount and sample size).
+    \item Read barcodes from a file.
+    \begin{itemize}
+      \item Give barcodes a name.
+    \end{itemize}
+    \item Cut a barcode from a read.
+    \begin{itemize}
+      \item Optionally select which part needs to be saved.
+    \end{itemize}
+  \end{itemize}
+
+  \vfill
+  Obsoletes: \bs{demultiplex}.
+\end{fframe}
+
+\section{Questions?}
+\lastpagetemplate
+\begin{frame}
+  \begin{center}
+    Acknowledgements:
+    \bigskip
+    \bigskip
+
+    Martijn Vermaat
+
+    Yahya Anvar
+
+    Johan den Dunnen
+  \end{center}
+\end{frame}
+
+\end{document}

lectures/packages/ul_logo.eps

+../../submodules/presentation/ul_logo.eps
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