Manual

You survived the installation? Great! Here is how you can use BobSeg...

First time use?

Before you can use BobSeg you have to get it onto the machine you installed all dependencies onto.

1. choose a folder to install BobSeg in. This will also become your active working folder. This might e.g. the folder /Users/goldsteinlab/Jug.
2. open a terminal and go to the folder we just created (cd /Users/goldsteinlab/Jug).
3. use git to get the latest version of BobSeg: git clone https://github.com/fjug/BobSeg.git.
   • Hint: from now on you can update BobSeg by going into /Users/goldsteinlab/Jug/BobSeg and execute the command git pull.

Launching jupyter

You can do all in several ways, but here I explain how to use BobSeg from within jupyter notebooks. In order to start jupyter, do this:

• Open a new terminal window (this window has to stay open all the time and will print lots of things you can usually ignore).
• Navigate to the BobSeg folder using cd _<folder>_, eg. cd /Users/goldsteinlab/Jug/BobSeg.
• Call jupyter-notebook from this terminal.
• Your default browser will open jupyter and put you in the folder you where at when you started jupyter.

2D pipeline