Merge branch 'master' of git.lumc.nl:humgen/ngs-intro-course

README.md

-# NGS Introduction Course
-This repository contains lectures and practicals for a one day introduction to
-NGS data analysis.
-
-## Organisation
-There are two submodules on which this repository depends.
-
-- **presentation** template for presentations in LaTeX.
-- **presentation-pics** repository containing pictures.
-
-The **website** directory is for storing the compiled presentations, handouts
-and program. A *Trac wiki markup* file contains the website content. Uploading,
-updating and adding attachments can be done easily with the
-[tracwiki](https://pypi.python.org/pypi/tracwiki) program.
-
-## Usage
-A new presentation can be added like this:
-
-    cd presentation
-    bash mkpres.sh ../mypresentation
-
-Pictures in the presentation can be made available by adding a symbolic link to
-the presentation-pics repository.
-
-    ln -s ../presentation-pics/pics/somepicture.png
-
-The Makefile will take care of converting this picture to the correct format.
+# NGS Introduction Course
+This repository contains lectures and practicals for a one day introduction to
+NGS data analysis.
+
+## Organisation
+There are two submodules on which this repository depends.
+
+- **[presentation](https://git.lumc.nl/j.f.j.laros/presentation)** template for presentations in LaTeX.
+- **[presentation-pics](https://git.lumc.nl/humgen/presentation-pics)** repository containing pictures.
+
+The **website** directory is for storing the compiled presentations, handouts
+and program. A *Trac wiki markup* file contains the website content. Uploading,
+updating and adding attachments can be done easily with the
+[tracwiki](https://pypi.python.org/pypi/tracwiki) program.
+
+## Usage
+After cloning this repository, fetch the data from the submodules by issuing the
+following two commands:
+
+    git submodule init
+    git submodule update
+
+([More on Git submodules](http://git-scm.com/book/en/Git-Tools-Submodules))
+
+A new presentation can be added like this:
+
+    cd presentation
+    bash mkpres.sh ../mypresentation
+
+Pictures in the presentation can be made available by adding a symbolic link to
+the presentation-pics repository.
+
+    ln -s ../presentation-pics/pics/somepicture.png
+
+The Makefile will take care of converting this picture to the correct format.
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