<commit_before># Analysis of Genetic Data 1: Setup

This description assumes that you have already registered for a
[user account on
midway](http://rcc.uchicago.edu/getting-started/request-account). If
you do not have an account, or if you plan to use a different
computing resource (e.g., your own computer), these steps will be
slightly different for you.

+ We will use
  [pair programming](http://dx.doi.org/10.1145/2492007.2492020) in
  this workshop. Introduce yourself to your partner and decide between
  you who will be the **driver** and who will be the
  **observer/navigator**.

+ We will use the University of Chicago
  [Google Docs](http://gdocs.uchicago.edu) to help make this workshop
  more interactive, and encourage discussion. Open up the
  [Google doc](http://tinyurl.com/h8y6p9p) in your Web browser, and
  introduce yourself.

+ Log on to midway using ssh with X forwarding:
  `ssh -X <EMAIL>`.

+ Request interactive session using reservation for this workshop. I
  suggest using screen in case you lose your connection.

+ Load the required modules.
  
```bash
module load R/3.2
```
  
+ Optionally, load R Studio. (Rest of workshop will assume that you
  are running R from console, but all the steps should work using R
  Studio as well.)

+ Clone the git repository (note you don't need a github account to do
this):

```bash<commit_msg>Added sinteractive step to Setup.<commit_after># Analysis of Genetic Data 1: Setup

This description assumes that you have already registered for a
[user account on
midway](http://rcc.uchicago.edu/getting-started/request-account). If
you do not have an account, or if you plan to use a different
computing resource (e.g., your own computer), these steps will be
slightly different for you.

+ We will use
  [pair programming](http://dx.doi.org/10.1145/2492007.2492020) in
  this workshop. Introduce yourself to your partner and decide between
  you who will be the **driver** and who will be the
  **observer/navigator**.

+ We will use the University of Chicago
  [Google Docs](http://gdocs.uchicago.edu) to help make this workshop
  more interactive, and encourage discussion. Open up the
  [Google doc](http://tinyurl.com/h8y6p9p) in your Web browser, and
  introduce yourself.

+ Log on to midway using ssh with X forwarding:
  `ssh -X <EMAIL>`.

+ Request interactive session using reservation for this workshop. I
  suggest using screen in case you lose your connection.

```bash
screen -S workshop-gda1
sinteractive --time=03:00:00 --reservation=workshop-3-nov-2016
```

+ Load the required modules.
  
```bash
module load R/3.2
```
  
+ Optionally, load R Studio. (Rest of workshop will assume that you
  are running R from console, but all the steps should work using R
  Studio as well.)

+ Clone the git repository (note you don't need a github account to do
this):

```bash
{'fraction_non_alphanumeric': 0.08491228070175438, 'fraction_numerical': 0.02245614035087719, 'mean_word_length': 3.9496527777777777, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1499968', 'n_tokens_mistral': 881, 'n_tokens_neox': 809, 'n_words': 388}