Merge branch 'jfjlaros_2014' into 'master'

Jfjlaros 2014

introduction/18333fig0101-tn.png

+../pics/src/18333fig0101-tn.png
\ No newline at end of file

introduction/18333fig0102-tn.png

+../pics/src/18333fig0102-tn.png
\ No newline at end of file

introduction/18333fig0103-tn.png

+../pics/src/18333fig0103-tn.png
\ No newline at end of file

introduction/introduction.tex

@@ -31,9 +31,8 @@
 
 % First page of the presentation.
 \section{Introduction}
-\begin{frame}
-  \frametitle{Version control.}
-
+\subsection{Version control}
+\begin{pframe}
   \emph{The management of changes to documents, computer programs, large web
   sites, and other collections of information.} --- Wikipedia.
   \bigskip
@@ -48,18 +47,16 @@
     \end{itemize}
     \item Enables collaboration.
   \end{itemize}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Why should I use it?}
+\end{pframe}
 
+\subsection{Why should I use it?}
+\begin{pframe}
   For a single user:
   \begin{itemize}
     \item Revert files to a previous state.
     \item Revert the entire project back to a previous state.
     \item Review changes made over time.
     \item Backup.
-    \item \ldots
   \end{itemize}
   \bigskip
   \pause
@@ -70,13 +67,11 @@
     \item Allow multiple people working on the same project at the same time.
     \item Conflict resolution.
     \item See who made which changes at which time.
-    \item \ldots
   \end{itemize}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Why should I not use it?}
+\end{pframe}
 
+\subsection{Why should I not use it?}
+\begin{pframe}
   A list of common excuses:
   \begin{itemize}
     \item It is too much work.
@@ -93,60 +88,53 @@
   \begin{itemize}
     \item I'm too busy rewriting the code I accidentally deleted.
   \end{itemize}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Local repository.}
+\end{pframe}
 
+\subsection{Local repository}
+\begin{pframe}
   \begin{figure}[]
     \begin{center}
       \colorbox{white}{
         \hspace{0.5cm}
-        \includegraphics[height=0.8\textheight]{pics/18333fig0101-tn}
+        \includegraphics[height=0.8\textheight]{18333fig0101-tn}
         \hspace{0.5cm}
       }
     \end{center}
     \caption{Local version control diagram.}
-    \label{}
   \end{figure}
-\end{frame}
+\end{pframe}
 
-\begin{frame}
-  \frametitle{Central repository.}
-  
+\subsection{Central repository}
+\begin{pframe}
   \begin{figure}[]
     \begin{center}
       \colorbox{white}{
         \hspace{0.5cm}
-        \includegraphics[height=0.8\textheight]{pics/18333fig0102-tn}
+        \includegraphics[height=0.8\textheight]{18333fig0102-tn}
         \hspace{0.5cm}
       }
     \end{center}
     \caption{Centralised version control diagram.}
-    \label{}
   \end{figure}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Distributed repositories.}
+\end{pframe}
 
+\subsection{Distributed repositories}
+\begin{pframe}
   \begin{figure}[]
     \begin{center}
       \colorbox{white}{
         \hspace{0.5cm}
-        \includegraphics[height=0.8\textheight]{pics/18333fig0103-tn}
+        \includegraphics[height=0.8\textheight]{18333fig0103-tn}
         \hspace{0.5cm}
       }
     \end{center}
     \caption{Distributed version control diagram.}
-    \label{}
   \end{figure}
-\end{frame}
+\end{pframe}
 
 \section{Git}
-\begin{frame}
-  \frametitle{The name.}
-
+\subsection{The name}
+\begin{pframe}
   \emph{Git (n): A person who is deemed to be despicable or contemptible.} ---
   WordNet.
   \bigskip
@@ -155,11 +143,10 @@
   \emph{I'm an egotistical bastard, and I name all my projects after myself.
   First ``Linux'', now ``git''.} --- Linus Torvalds.
   \bigskip
-\end{frame}
-
-\begin{frame}
-  \frametitle{History.}
+\end{pframe}
 
+\subsection{History}
+\begin{pframe}
   Designed to replace the commercial package \emph{BitKeeper}.
   \begin{itemize}
     \item Speed.
@@ -170,12 +157,11 @@
     \item Able to handle large projects like the Linux kernel efficiently
       (speed and data size).
   \end{itemize}
-\end{frame}
+\end{pframe}
 
 \section{Remotes}
-\begin{fframe}
-  \frametitle{A lot of choices.}
-
+\subsection{A lot of choices}
+\begin{pframe}
   GitHub.
   \begin{itemize}
     \item Only free for open source projects.
@@ -196,25 +182,30 @@
 
   \vfill
   \permfoot{https://github.com/}
-\end{fframe}
+\end{pframe}
 
 \section{Practical}
-\begin{fframe}
-  \frametitle{Outline.}
-
+\subsection{Outline}
+\begin{pframe}
   We are going to:
   \begin{itemize}
     \item Create and configure a user account on the GitLab server.
     \item Upload an \bt{ssh-key} to work with Git.
   \end{itemize}
+  \bigskip
+
+  Or alternatively, if you can not access the internal network:
+  \begin{itemize}
+    \item Use \bt{https} to work with GitLab.
+  \end{itemize}
 
   \vfill
   \permfoot{https://git.lumc.nl/}
-\end{fframe}
+\end{pframe}
 
 \section{Questions?}
 \lastpagetemplate
-\begin{fframe}
+\begin{pframe}
   \begin{center}
     Acknowledgements:
     \bigskip
@@ -222,12 +213,12 @@
 
     Martijn Vermaat
 
-    Zuotian Tatum
+    Wibowo Arindrarto
 
+    Zuotian Tatum
   \end{center}
 
   \vfill
   \permfoot{https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/git}
-\end{fframe}
-
+\end{pframe}
 \end{document}

introduction/introduction_handouts.tex

@@ -14,7 +14,7 @@ Git Introduction practical.
 \end{center}
 \bigskip
 
-\subsubsection*{Local configuration.}
+\subsubsection*{Local configuration}
 First, let Git know what your name and e-mail address is:
 \begin{lstlisting}
   $ git config --global user.name "<Your Name>"
@@ -23,6 +23,24 @@ First, let Git know what your name and e-mail address is:
 \end{lstlisting}
 \bigskip
 
+For the other practicals, it is convenient to have a \texttt{projects} folder
+for your repositories:
+\begin{lstlisting}
+  mkdir ~/projects
+  cd ~/projects
+\end{lstlisting}
+
+\newcommand{\generalconfiguration}{
+  You can now edit your profile by clicking on the ``profile'' button
+  (pictogram of a torso), located on the top right of your screen. On mouse
+  over, a text balloon will pop up, saying ``Profile settings''.
+  \medskip
+
+  Check your name and e-mail address (you probably want to change your name).
+  \bigskip
+}
+
+\subsubsection*{Remote configuration for LUMC participants}
 Check whether you have an ssh key:
 \begin{lstlisting}
   $ cat ~/.ssh/id_rsa.pub
@@ -37,26 +55,46 @@ If not, make one:
   Enter same passphrase again:
 \end{lstlisting}
 You can leave all fields blank.
+\bigskip
 
-\subsubsection*{Remote configuration.}
 Open \texttt{https://git.lumc.nl} in your browser.
-\bigskip
+\medskip
 
 In the authentication form, use your LUMC username and password (LDAP login).
 \bigskip
 
-You can now edit your profile by clicking on the ``profile'' button (pictogram
-of a torso), located on the top right of your screen. On mouse over, a text
-balloon will pop up, saying ``My profile''.
+\generalconfiguration
+
+To be able to upload new versions, you need to add your ssh key. Open the ``SSH
+Keys'' tab and click the ``Add SSH Key'' button.
+\medskip
+
+Give your key a title (e.g., ``Course laptop'').
+\medskip
+
+Copy your ssh key to the key field (see the \texttt{cat} command above).
+
+\subsubsection*{Remote configuration for other participants}
+Open \texttt{https://git.lumc.nl} in your browser.
 \bigskip
 
-Check your name and e-mail address (you probably want to change your name).
+In the authentication form, use the provided username and password (Standard
+login).
 \bigskip
 
-To be able to upload new versions, you need to add your ssh key. Click the
-``Add Public Key'' button.
+\generalconfiguration
 
-Give your key a title (e.g., ``Course Laptop'').
+Open \texttt{https://git.lumc.nl/humgen/gitcourse} in your browser.
+\bigskip
 
-Copy your ssh key to the key field (see the \texttt{cat} command above).
+On the right, you see a text box containing the string
+\texttt{git@git.lumc.nl:humgen/gitcourse.git}, notice the ``SSH'' button is
+selected. During the course we will ask you to use this protocol (ssh) for
+remote repositories. Since we do not have access to the LUMC using this
+protocol, we are going to use an other protocol.
+\bigskip
+
+Click the ``HTTPS'' button, and you will see the string
+\texttt{https://git.lumc.nl/humgen/gitcourse.git}. We can use this protocol
+(https) for remote repositories.
 \end{document}

introduction/pics

-../pics/
\ No newline at end of file

skeleton/skeleton.tex

@@ -2,7 +2,7 @@
 
 \title{Analysis projects skeleton}
 \providecommand{\myConference}{Git course}
-\providecommand{\myDate}{Monday, October 14, 2013}
+\providecommand{\myDate}{Monday, June 23, 2014}
 \author{Jeroen F. J. Laros}
 \providecommand{\myGroup}{Leiden Genome Technology Center}
 \providecommand{\myDepartment}{Department of Human Genetics}
@@ -31,9 +31,8 @@
 
 % First page of the presentation.
 \section{Introduction}
-\begin{frame}
-  \frametitle{Shared projects.}
-
+\subsection{Shared projects}
+\begin{pframe}
   Most of us work on multiple projects with multiple people.
   \bigskip
 
@@ -48,12 +47,11 @@
     \pause
     \item Have the same structure for all projects.
   \end{itemize}
-\end{frame}
+\end{pframe}
 
 \section{Starting a project}
-\begin{fframe}
-  \frametitle{Project skeleton.}
-
+\subsection{Project skeleton}
+\begin{pframe}
   Usage:
   \begin{itemize}
     \item Make a \emph{fork} (copy) of the skeleton project.
@@ -76,11 +74,10 @@
 
   \vfill
   \permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
-\end{fframe}
+\end{pframe}
 
-%\begin{fframe}
-%  \frametitle{Forking}
-%
+%\subsection{Forking}
+%\begin{pframe}
 %  Make a new analysis project.
 %  \begin{itemize}
 %    \item Go to the ``Project skeleton'' project page on our GitLab server.
@@ -93,11 +90,10 @@
 %  
 %  \vfill
 %  \permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
-%\end{fframe}
+%\end{pframe}
 
-%\begin{frame}
-%  \frametitle{Configuration}
-%
+%\subsection{Configuration}
+%\begin{pframe}
 %  Configure your project.
 %  \begin{itemize}
 %    \item Choose to make your project public or not.
@@ -107,12 +103,11 @@
 %    \end{itemize}
 %    \item Add the people that work on this project.
 %  \end{itemize}
-%\end{frame}
+%\end{pframe}
 
 \section{Project structure}
-\begin{frame}
-  \frametitle{Global overview.}
-
+\subsection{Global overview}
+\begin{pframe}
   Project layout:
   \begin{itemize}
     \item analysis
@@ -123,22 +118,20 @@
   \bigskip
 
   Ideally, every directory in the project has a \bt{README} file.
-\end{frame}
-
-\begin{frame}
-  \frametitle{The toplevel \bt{\,README\,\,} file.}
+\end{pframe}
 
+\subsection{The toplevel ``README'' file}
+\begin{pframe}
   This file contains general information about the project, for example:
   \begin{itemize}
     \item Who leads the project.
     \item Who participates in the project.
     \item The amount of hours people have spent on this project.
   \end{itemize}
-\end{frame}
-
-\begin{frame}
-  \frametitle{The \bt{\,doc\,\,} directory.}
+\end{pframe}
 
+\subsection{The ``doc'' directory}
+\begin{pframe}
   Documentation on the project:
   \begin{itemize}
     \item Annotation of the data.
@@ -148,11 +141,10 @@
       \item You may want to note who provided the documentation.
     \end{itemize}
   \end{itemize}
-\end{frame}
-
-\begin{frame}
-  \frametitle{The \bt{\,data\,\,} directory.}
+\end{pframe}
 
+\subsection{The ``data'' directory}
+\begin{pframe}
   Used to store all raw data.
   \bigskip
 
@@ -176,11 +168,10 @@
     \end{itemize}
   \end{itemize}
 
-\end{frame}
-
-\begin{frame}
-  \frametitle{The \bt{\,analysis\,\,} directory.}
+\end{pframe}
 
+\subsection{The ``analysis'' directory}
+\begin{pframe}
   All analysis related files are stored here:
   \begin{itemize}
     \item Run scripts.
@@ -195,22 +186,20 @@
     \item Normal data analysis.
     \item $k$-mer analysis.
   \end{itemize}
-\end{frame}
-
-\begin{frame}
-  \frametitle{The \bt{\,src\,\,} directory.}
+\end{pframe}
 
+\subsection{The ``src'' directory}
+\begin{pframe}
   Any custom scripts and specific software versions for this project.
   \bigskip
 
   When these scripts are useful for other projects, move them to their own
   repository.
-\end{frame}
+\end{pframe}
 
 \section{Working with large files}
-\begin{fframe}
-  \frametitle{Git is not designed for massive files.}
-
+\subsection{Git is not designed for massive files}
+\begin{pframe}
   Some problems with large files:
   \begin{itemize}
     \item Limited storage on the server.
@@ -231,11 +220,10 @@
 
   \vfill
   \permfoot{http://git-annex.branchable.com/}
-\end{fframe}
-
-\begin{frame}[fragile]
-  \frametitle{Git annex.}
+\end{pframe}
 
+\subsection{Git annex}
+\begin{pframe}
   Manage files with git, without checking their contents in.
   \begin{itemize}
     \item Manage large files without storing them.
@@ -251,11 +239,10 @@
   \begin{lstlisting}[language=none, caption=Enable git-annex.]
     $ git annex init "<name>"
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Adding big files.}
+\end{pframe}
 
+\subsection{Adding big files}
+\begin{pframe}
   In our master repository, we annex a file.
   \bigskip
 
@@ -274,11 +261,10 @@
     <filename>: broken symbolic link to ...
     $ git annex get <filename>
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Removing files.}
+\end{pframe}
 
+\subsection{Removing files}
+\begin{pframe}
   As long as there are enough copies available, you can remove files.
   \bigskip
 
@@ -297,11 +283,10 @@
     $ rm -rf <repository>
     rm: cannot remove <repository>/.git/annex/objects/...
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Synchronise your results.}
+\end{pframe}
 
+\subsection{Synchronise your results}
+\begin{pframe}
   Let the other repositories know what you have done.
   \bigskip
 
@@ -317,11 +302,10 @@
   \begin{lstlisting}[language=none, caption=Synchronise with a selection.]
     $ git annex sync origin
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Working together on the same clone.}
+\end{pframe}
 
+\subsection{Working together on the same clone}
+\begin{pframe}
   Sometimes you need to work with other people on the same repository clone.
   \begin{itemize}
     \item Where the large files are stored.
@@ -335,11 +319,11 @@
     $ find -type d -exec chmod 775 {} \;
     $ find -type f -exec chmod 664 {} \;
   \end{lstlisting}
-\end{frame}
+\end{pframe}
 
 \section{Questions?}
 \lastpagetemplate
-\begin{fframe}
+\begin{pframe}
   \begin{center}
     Acknowledgements:
     \bigskip
@@ -353,7 +337,7 @@
 
   \vfill
   \permfoot{http://git-annex.branchable.com/}
-  \permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
-\end{fframe}
 
+  \permfoot{https://git.lumc.nl/lgtc-bioinformatics/project-skeleton}
+\end{pframe}
 \end{document}

website/.gitignore

+.trac_config

website/.trac_config

-{"username": "jfjlaros", "info": {"git": [15, "e7cdcdf9234d9e40e42159594b5ba041"]}, "protocol": "https", "location": "humgenprojects.lumc.nl/trac/humgenprojects"}
\ No newline at end of file