This is an old revision of the document!
Make a new project directory:
# Log into summit $ ssh scompile # Navigate to the space where you want to put your directory. I'm putting mine in /scratch/summit/<eID>@colostate.edu/DSCI512_RNAseq # Make a new directory & navigate into it: $ mkdir PROJ04_yeastDemo $ cd PROJ04_yeastDemo
Populate the project directory with relevant sub-directories:
$ mkdir 01_input $ mkdir 02_scripts $ mkdir 03_output
Copy relevant input files:
$ cd 01_input $ cp /firstname.lastname@example.org/DATA_DSCI512/*.fastq . $ cp /email@example.com/DATA_DSCI512/metadata_aceticAcid_subset.txt . $ ls
Explore the files.
Navigate to the directory where you originally downloaded David's github repository.
$ cd /scratch/summit/<eID>@colostate.edu/DSCI512_RNAseq $ cd PROJ01_testsummit $ cd summit-rna-seq-setup
Pull updates from the repository.
# Update the folder $ git pull
Copy the updated file activate.bashrc higher up so it is easier to access.
$ cp activate.bashrc /scratch/summit/<eID>@colostate.edu/ # Replace <eID> with your eID
Learn how to load the software
$ source /scratch/summit/<eID>$colostate.edu/activate.bashrc
Common pitfall: This code needs to be executed from scompile. If something goes strangely, try to
ssh compile and then try it again.
Quick tip: Anytime we want to use any of this software in a script, we'll have to add this source command within the code so that the software is accessible.
Major question: Does this really install software?
It gets really tiresome to type
squeue -u $USER. Let's shorten it to
$ alias scheck='squeue -u $USER'
That will let you type
scheck anytime during this summit session. Every time you log in, you'll need to re-do the aliasing. Alternatively, if you want to make it permanent, you can add that line of code to the end of a file in your home directory:
My .bash_profile looks like this at the end:
#Aliases alias scheck="squeue -u $USER" # Remove this if you don't want to display README at login if [ -f ~/README.mdwn ]; then cat ~/README.mdwn fi
Before the changes to your updated .bash_profile will take place, you'll need to either log out and log back in again, or source your new .bash_profile with the following line of code:
$ source .bash_profile
CAUTION! Be very careful updating your .bash_profile file. Make backup copies of this before you alter it. Especially if you do this on your local computer, you can mess up your computer.