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 /email@example.com/DATA_DSCI512/*.fastq . $ cp /firstname.lastname@example.org/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
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.
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