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feat: added selecting workflows section
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‎slides/creators/Selecting_Workflows.tex

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\section{Selecting Curated Workflows}
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{
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\usebackgroundtemplate{
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\vbox to \paperheight{\vfil\hbox to \paperwidth{\hfil\includegraphics[height=.7\paperheight]{example_dags/rulegraph_complex.png}\hfil}\vfil}
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}
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\frame{
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\frametitle{Selecting Workflows}
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\begin{mdframed}[tikzsetting={draw=white,fill=white,fill opacity=0.8,
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line width=0pt},backgroundcolor=none,leftmargin=0,
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rightmargin=150,innertopmargin=4pt,roundcorner=10pt]
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\tableofcontents[currentsection,sections={1-4},hideothersubsections]
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\end{mdframed}
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}
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}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}
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\frametitle{What is this about?}
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\begin{question}[Questions]
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\begin{itemize}
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\item How do I get a workflow for a given scientific problem?
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\item How do I run such an arbitrary workflow?
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\end{itemize}
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\end{question}
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\begin{docs}[Objectives]
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\begin{enumerate}
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\item Introducing the workflow catalogue!
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\item Learning the difference between ``curation'' (what some people think) and ``curation'' (what really works).
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\end{enumerate}
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\end{docs}
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\end{frame}
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\subsection{The Snakemake Workflow Catalogue}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}
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\frametitle{Selecting and Downloading from the Workflow Catalogue}
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You can find the \Snakemake{} worfkflow catalogue, \lhref{https://snakemake.github.io/snakemake-workflow-catalog/?rules=true}{here}. It makes a difference between workflows which meet best-practice criteria - and those which do not.\newline
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\begin{columns}
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\begin{column}{0.5\textwidth}
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You can download and run any workflow. \Snakemake's portability features ensure it will work everywhere $\ldots$\pause
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\begin{warning}
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$\ldots$ except, you most likely cannot, because of a missing cluster configuration.
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\end{warning}
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\end{column}
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\begin{column}{0.5\textwidth}
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\includegraphics[width=\textwidth]{Snakemake/Snakemake_Workflow_Catalog.png}
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\end{column}
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\end{columns}
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}
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\frametitle{Searching \emph{your} Workflow}
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\begin{columns}
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\begin{column}{0.5\textwidth}
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\includegraphics[width=\textwidth]{Snakemake/Searching_Workflows_in_Catalog.png}
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\end{column}
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\begin{column}{0.5\textwidth}
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You can look for
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\begin{itemize}
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\item topical keywords and
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\item software
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\end{itemize}
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\end{column}
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\end{columns}
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}
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\frametitle{Workflows Compliance}
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\begin{question}[Noted this?]
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\includegraphics[width=0.8\textwidth]{Snakemake/Snakemake_Workflow_Catalog_Categories.png}
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\end{question}
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}[fragile]
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\frametitle{Deployment}
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Select (=click on) any desired workflow. There are three alternatives:
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\begin{enumerate}[<+->]
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\item a workflow offers a release - in which case you can download and unpack it
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\item all workflows offers a ``\altverb{git clone}'' hint
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\item or you use the \altverb{snakedeploy} to get everything you need.
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\end{enumerate}
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}[fragile]
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\frametitle{Deployment II - Creating an Environment Fork}
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Usually, we can create an environment like:
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\begin{lstlisting}[language=Bash, style=Shell]
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$ mamba create -c conda-forge -c bioconda -n snakemake \
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> snakemake snakemake-executor-plugin-slurm \
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> snakemake-storage-plugin-fs
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\end{lstlisting}
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This should install a \Snakemake{} environment with all necessary tools!
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}[fragile]
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\frametitle{Deployment III - First Step!}
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Follow step 2 of a selected workflow usage instructions:
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\begin{columns}
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\begin{column}{0.4\textwidth}
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\centering
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\includegraphics[width=0.95\textwidth]{Snakemake/deploy_workflow}
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\end{column}
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\begin{column}{0.6\textwidth}
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A usual command is:
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\begin{lstlisting}[language=Bash, style=Shell]
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$ snakedeploy deploy-workflow \
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> <URL>
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\end{lstlisting}
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This will create the directories \altverb{workflow} and \altverb{config} in your current directory.
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\begin{hint}
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Alternatively, you may navigate to the repository of your desired workflow and download the entire workflow.
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\end{hint}
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\end{column}
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\end{columns}
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}[fragile]
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\frametitle{Finalizing the Deploymment}
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We could now deploy our sample workflow:
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\begin{itemize}
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\item Please create a directory \altverb{mkdir -p ~/example_workflow}
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\item Change to this directory.
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\item Deploy our sample workflow with
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\end{itemize}
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\begin{lstlisting}[language=Bash, style=Shell]
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$ snakedeploy deploy-workflow \
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> <++course.deploy_url++>
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\end{lstlisting}
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}[fragile]
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\frametitle{Running Workflows on Cluster (or other environment)}
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Most likely a specific workflow never has been testing on \emph{your} computer before. It is almost ensured it will run on arbitrary servers, but clusters are a different story. \newline
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So
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\begin{itemize}[<+->]
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\item try to parameterize your workflow as we will learn and create a "profile"
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\item if it gives issues and you know how to correct it, ``fork'' the worklow and create a pull request
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\item if you cannot fix it, create a bug report
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\end{itemize}
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}
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\frametitle{\Interlude{Learn git!}}
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If you do not know what ``fork'' and ``pull request'' means, learn git!
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\begin{itemize}[<+->]
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\item there are courses
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\item and lots of online material
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\item and books
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\end{itemize}
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\pause
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\begin{warning}
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Knowing git is essential in data analysis!
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\end{warning}
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\end{frame}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}[fragile]
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\frametitle{\HandsOn{Configuring the Workflow}}
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It is now time to configure and parameterize the workflow.
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\pause
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\begin{hint}
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As the configuration is workflow dependent you need to follow instructions, now.
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\end{hint}
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\pause
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Eventually start the workflow using:
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\begin{lstlisting}[language=Bash, style=Shell]
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$ snakemake --executor slurm \
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> -j unlimited \
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> --configfile <path to file> \
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> --workflow-profile <path to directory> \
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> --directory <path to your course output>
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\end{lstlisting}
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\pause
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\begin{hint}
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We will learn a few tricks to shorten this line.
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\end{hint}
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\end{frame}
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