Problem Sets

Problem Set 1: Now available. Due: 1/27/16 at 11:59pm.
Problem Set 2: Now available. Due: 2/10/16 at 11:59pm.
Problem Set 3: Now available. Due: 2/24/16 at 11:59pm.


Instructions for submitting problem sets

1. Getting your files onto corn/Logging onto corn using a terminal

First you will need to put all the the files you want to submit in a single directory on corn. Make sure you do not have any extra files in that directory or they will also get submitted!

Windows Users

If you are unfamiliar with working on a remote server using Windows,here is a short tutorial that explains how to get set up.

Mac and Linux Users

If you did the problem set on corn (i.e. wrote and tested your code there), just make sure you gather the submission files in a single directory and you can go to step 3.

If you worked on the problem set on your local machine, start by putting everything in a single directory. Then open a terminal (If you're on a mac and do not know where the terminal application is, type command-space and search for “terminal”). At the prompt (the $ that you see at the end of the lines that are printed in the terminal window) if you type “ls” (stands for list) then hit enter, you'll see all the files and directories in your home directory. For instance, I see the following:

$ ls
ABBYY        Documents    Library      Pictures     projects
Applications Downloads    Movies       Public       software
Desktop      Dropbox      Music        ncbi

Go to the directory that contains the directory with your submission using “cd” (stands for change directory). Say you put your problem set files in /Users/yourusername/courses/bmi217/pset1 then you would type:

$ cd /Users/yourusername/courses/bmi217

Now if you type “ls” you should see the directory that contains your files for submission. To copy this directory onto corn, type the following (replace pset1 with your actual directory name and fill in your actual sunet):

$ scp -r pset1 yoursunet@corn.stanford.edu:~/

You may see a warning message asking if you want to continue. Type yes and hit enter. Then you will be prompted for your password. Enter the your sunet password. You've move the files over, so now we will log into corn!

Enter the following at the prompt:

ssh yoursunet@corn.stanford.edu

You may see the warning again (enter yes if you do) and will be asked for your password. Once you have logged in, check that your problem set directory is there by typing “ls” at the prompt.

2. Testing your code on corn

First navigate to the directory with your submission files - we'll call it pset1 here - and check that you have everything you want to submit (and nothing else!).

$ cd pset1
$ ls
PS1.pdf         gwas.R       parsePlink.R readme.txt

Run your code to make sure it outputs what you expect and does not generate any errors. One way to do this is to start R and run the source() command. For instance, to test my first R script I could do:

$ R
[You'll see the output of R starting up, then the R prompt (">")]
> source("gwas.R")

Be sure to test all of your scripts if you have more than one. Exit R when you're done by typing CTRL-D.

3. Running the submission script

From within the directory that contains your submission files, type the following at the prompt to submit problem set 1:

$ /usr/class/biomedin217/bin/submit p1

To submit problem sets 2 through 4, you will use “p2”, “p3”, and “p4”, respectively, instead of “p1”. To test the submission process you can use “test” instead of “p1”. We will not look at test submissions, but we recommend you test out the submission script early if this is your first time using this type of submission process.

You will see many lines of output that end with “Submission completed”.

That means everything worked, so you are all set!

You can logout of corn by typing exit at the prompt.

If you have any issues, post on Piazza, ask your friends or come to office hours.

ĉ
Peyton Greenside,
Jan 17, 2016, 10:57 AM
Ċ
Daniel Kim,
Feb 3, 2016, 10:52 PM
ċ
pset3.zip
(3078k)
Diego Calderon,
Feb 20, 2016, 6:51 PM
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