Added documentation.

README.md

+# Project skeleton
+A skeleton Git repository for analysis projects.
+
+# Preparations
+Install dependencies.
+
+```bash
+pip install cookiecutter
+pip install python-gitlab
+```
+
+Configure Cookiecutter by editing `.cookiecutterrc` in your home directory.
+
+```yml
+---
+default_context:
+  full_name: Your Name
+  email: UserName@lumc.nl
+cookiecutters_dir: /path/to/cookiecutters/
+```
+
+Configure Python GitLab by editing `.python-gitlab.cfg` in your home directory.
+
+```INI
+[global]
+default = gitlab
+ssl_verify = true
+timeout = 5
+
+[gitlab]
+url = https://git.lumc.nl
+private_token = your_token_here
+```
+
+# Starting a project
+To start a new analysis project based on this skeleton, follow the following
+steps:
+
+```bash
+cookiecutter https://git.lumc.nl/sasc/cookiecutter-data-analysis.git
+```
+
+## Working together on the same clone
+If you need to work with other people on the same repository clone on the Shark cluster, you can use the following command to give group access:
+
+```bash
+find -type d -exec chmod 775 {} \;
+find -type f -exec chmod 664 {} \;
+```
+
+## Cloning to a portable disk (NTFS)
+Presuming your disk is attached to your own computer and the repository is on
+the Shark cluster, you can use the following commands.
+
+    git clone ssh://shark/path/to/project/my-project
+    cd my-project
+
+For some reason `annex-ignore` is set to `true`, we need to set it to `false`.
+
+    git config remote.origin.annex-ignore false
+
+Set the repository to *direct mode* to prevent making symlinks, otherwise it
+will be very difficult for windows users to access the files.
+
+    git annex direct
+
+SSH caching seems to be broken on NTFS.
+
+    git config annex.ssh-options "-S /tmp/ssh_mux_%h_%p_%r"
+
+Or alternatively, disable SSH caching all together (slow when working with a
+large number of files).
+
+    git config annex.sshcaching false
+
+Get the content.
+
+    git annex get .