Better url handling.

presentation @ 958e0fcf

-Subproject commit cb4d87fdf0fc91ed8d121305fec03b26eb82316b
+Subproject commit 958e0fcff339edbd4d21ed0d6644f4141452e337

combining_tools/combining_tools.tex

@@ -413,7 +413,7 @@
   \end{itemize}
 
   \vfill
-  \permfoot{http://galaxy.psu.edu/}
+  \permfoot{\url{http://galaxy.psu.edu/}}
 \end{pframe}
 
 \begin{pframe}

command_practical/command_practical.tex

 \documentclass{article}
-\usepackage{geometry}
-\usepackage{listings}
-\usepackage{graphicx}
-
-\input{../shared/variables.tex}
 \input{../shared/practical.tex}
 
-\setlength{\parindent}{0pt}
-\frenchspacing
-
 \title{\courseTitle\\
   {\Large Practical Linux and NGS tools}}
 \date{\dayOne}
@@ -286,7 +278,7 @@ an idea of the metrics of this set of reads.
 
 FastQC also generates an HTML file. We have put the output somewhere online
 for
-you\footnote{https://barmsijs.lumc.nl/NGS-course/course.fq\_fastqc/fastqc\_report.html}.
+you\footnote{\url{https://barmsijs.lumc.nl/NGS-course/course.fq_fastqc/fastqc_report.html}}.
 
 % Alignment
 \subsection{Alignment with Bowtie}
@@ -459,7 +451,7 @@ a try to see the effect on the output you get.
 \medskip
 
 Like FastQC, VEP also creates an HTML file. We have put this online for
-you\footnote{https://barmsijs.lumc.nl/NGS-course/VEP\_summary.html}.
+you\footnote{\url{https://barmsijs.lumc.nl/NGS-course/VEP_summary.html}}.
 \medskip
 
 % End of practical

connecting/connecting.tex

@@ -175,7 +175,7 @@
   \end{itemize}
 
   \vfill
-  \permfoot{http://www.chiark.greenend.org.uk/~sgtatham/putty}
+  \permfoot{\url{http://www.chiark.greenend.org.uk/~sgtatham/putty}}
 \end{pframe}
 
 \begin{pframe}
@@ -279,7 +279,7 @@
   \end{figure}
 
   \vfill
-  \permfoot{http://en.wikipedia.org/wiki/IBM\_Roadrunner}
+  \permfoot{\url{http://en.wikipedia.org/wiki/IBM\_Roadrunner}}
 \end{pframe}
 
 \begin{pframe}

galaxy_practical/galaxy_practical.tex

 \documentclass{article}
-\usepackage{geometry}
-\usepackage{listings}
-\usepackage{graphicx}
-
-\input{../shared/variables.tex}
 \input{../shared/practical.tex}
 
-\setlength{\parindent}{0pt}
-\frenchspacing
-
 \title{\courseTitle\\
   {\Large Pipelines in Galaxy}}
 \date{\dayTwo}
@@ -38,7 +30,7 @@ Penn State's Galaxy is a useful way of wrapping many command line modules
 together in a user-friendly GUI. Galaxy is a web-based system so that you do
 not need to install any client side application. What you need is just to open
 your favourite webbrowser (firefox, IE, etc.) and access the galaxy server
-hosted at page (\texttt{https://usegalaxy.org/}). When logged in, you can save
+hosted at page (\url{https://usegalaxy.org/}). When logged in, you can save
 your workflow and execute the entire workflow on a new dataset without manually
 executing each individual step. You can also easily share these workflows with
 others.
@@ -64,7 +56,7 @@ the figure below.
 %\newpage
 
 \subsection{Availability and examples} The tools used in these exercises are all
-free for download, including Galaxy itself (\texttt{http://galaxyproject.org/}),
+free for download, including Galaxy itself (\url{http://galaxyproject.org/}),
 BWA for alignment, and FreeBayes for variant calling.
 
 \subsection{Note on test data} Data used in this practical is test data and not
@@ -106,7 +98,7 @@ this analysis possible within the time permitted.
 \section{Preparations.}
 
 \begin{enumerate}
-  \item Open a browser and go to \texttt{https://usegalaxy.org/}
+  \item Open a browser and go to \url{https://usegalaxy.org/}
   \item Register to gain access to data libraries and workflows.
   \begin{itemize}
     \item Click on ``User'', then on ``Register'' in the top bar.
@@ -180,7 +172,7 @@ Ensemble Variant Effect Predictor:
 \begin{itemize}
   \item In your history view, find the filtered VCF data. Right-click on its
     download button (floppy disk icon) and choose ``Copy link location''.
-  \item Go to \texttt{http://grch37.ensembl.org/}, click on the ``Variant
+  \item Go to \url{http://grch37.ensembl.org/}, click on the ``Variant
     Effect Predictor'' button, and click the big ``Launch Ve!P'' button.
   \item Under ``New VEP job'', paste the URL you just copied from Galaxy in
     the ``Or provide file URL'' field and click ``Run''.

shared/practical.tex

+\usepackage{geometry}
+\usepackage{listings}
+\usepackage{graphicx}
+\usepackage{hyperref}
+\hypersetup{
+  pdfborder={0 0 0}
+}
+
+\input{../shared/variables.tex}
+
+\setlength{\parindent}{0pt}
+\frenchspacing
+
 \lstset{
   basicstyle=\bf\ttfamily
 }

shared/variables.tex

@@ -8,8 +8,8 @@
 
 \newcommand{\baseWebsite}
   {https://humgenprojects.lumc.nl/trac/humgenprojects/wiki}
-\newcommand{\courseWebsite}{\baseWebsite/NGS-intro}
-\newcommand{\practicalWebsite}{\baseWebsite/NGS-intro-prep}
+\newcommand{\courseWebsite}{\url{\baseWebsite/NGS-intro}}
+\newcommand{\practicalWebsite}{\url{\baseWebsite/NGS-intro-prep}}
 
 \newcommand{\sponsorOne}{lgtc}