V-1. Download example dataset and notebooks

export PATH=/home/hmkang/bioboot/bin:${PATH} 
export PATH=/scratch/biobootcamp_fluxod/remills/anaconda/bin:${PATH}

Navigate to your bootcamp scratch directory (cd /scratch/biobootcamp_fluxod/UNIQUENAME). If a directory with your uniquename does not exist, make it using
```
mkdir /scratch/biobootcamp_fluxod/UNIQUENAME
cd /scratch/biobootcamp_fluxod/UNIQUENAME
  
```
Once in your directory, create a subdirectory for today’s segment
```
mkdir day4_cluster
cd day4_cluster
```

download the data for today to FLUX

Note that you can view a render of this notebook directly on GitHub as well!

wget https://github.com/bioboot/web-2015/raw/gh-pages/class-material/read_counts_by_region.tar.gz
tar zxvf read_counts_by_region.tar.gz
cd read_counts_by_region

For this exercise, we will need to run ipython notebook on flux. As with yesterday, start a notebook server with the following commands
- Start a notebook server
- Notes:
  1. you need to know which host you’re on. The command line prompt will show this (e.g., flux-login3)
  2. you need to know which port your instance of ipython listens to. The first few lines of output from ipython notebook will list this for you.
```
remills@flux-login3:/scratch/biobootcamp_fluxod/remills/biobootcamp$ ipython notebook --ip=flux-login3 --no-browser

[I 13:26:18.660 NotebookApp] Using MathJax from CDN: https://cdn.mathjax.org/mathjax/latest/MathJax.js
[I 13:26:19.220 NotebookApp] The port 8888 is already in use, trying another random port.
[I 13:26:19.473 NotebookApp] Serving notebooks from local directory: /scratch/biobootcamp_fluxod/kitzmanj
[I 13:26:19.473 NotebookApp] 0 active kernels
[I 13:26:19.473 NotebookApp] The IPython Notebook is running at: http://flux-login3:8889/
[I 13:26:19.473 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
```
- A word of warning: in general, running on the head node of the flux cluster is not a good practice, because the head node controls the job queue for the entire cluster. Instead you would want to enter the queue, login to a compute node, and do your work there.
- Now, your own ipython server is running on flux. But you will need to open a tunnel to get there. The below command will securely connect port 8889 on the computer flux-login3 to port 9000 on my computer.
```
 ssh -L localhost:9000:flux-login3:8889 YOURNAME@flux-login.engin.umich.edu
 
```
- Navigate to http://localhost:9000 and make a new notebook
Ipython notebook reminders:
- Green box - marks active cell. You are in EDIT mode.
- Hit escape to exit mode mode and go to COMMAND mode.
- In command mode:
  - A : insert new cell above
  - B : insert new cell below
  - Enter : edit the currently selected cell
  - up/down arrow : navigate up or down
- In either:
  - Shift-Enter : run the current cell
- Remember, you can run commands out of order in the notebook.