Text in red indicates a warning that you must not defy.
Text in bold and green denotes that it requires modification for individual users i.e. do not simply copy and paste without properly adapting it first.
Text in bold and orange denote that is requires modification for At vs. Soy work.
Creating subdirectories
Now that you are in your home directory, you need to begin to organize it with your projects to make working directories.
You will be analyzing an Arabidopsis (Arabidopsis thaliana, "At") project, a Soybean (Glycine max, "Soy") project and you individual Soybean Project for your Final Portfolio ("Portfolio"). Let's make three directories: one for At, one for Soy, and one for your Portfolio:
mkdir At
mkdir Soy
mkdir Portfolio
Confirm that these were made by listing ls what you have added to your working directory
ls
You should see At, Soy and Portfolio in blue text along the same line
Use the command to list longhand ll to see more information about what has been added to your working directory
ll
This time you should see At, Soy and Portfolio listed on separate lines with information about each directory. You will use each of these as your project working directories. All of the code and scripts provided for Arabidopsis in this class will be written so that you are running jobs in your At project directory.
We will go step by step through an analysis pipeline for an Arabidopsis RNA data set and in your research teams you will adapt these lessons for Soybean and Portfolio RNA datasets.
Let's set up your At working directory. As a beginner it is recommended to be in the location you are working so move into you At directory:
cd At
Whenever you change locations, get into the habit of checking by printing your working directory AKA your current location
pwd
It is critical that you organize your working directory so that your scripts can run without error.
Imagine you need to give directions to a friend to navigate your computer desktop to find a file you have saved. The HPC is your friend, and you need to tell the HPC where to find your data and where to put new processed data in Linux code.
Start out listing ls at what is currently set up in your At working directory
ls
You should see nothing return as a response.. that can be unsatisfying
Use the command to list longhand ll to see a sum total of 0 files or folders in your At working directory
ll
This time you should see a response of " total 0 "
Add folders to direct the HPC to find data files (AKA input) and where the HPC will write the new computed files (AKA output).
It is difficult to make an organized working directory your first time around. As you do more HPC work, you will get a sense of designing your own workflow to adapt codes efficiently and in a way that makes sense to you.
You will make the following directories named:
AlignedToTranscriptome
fastqc
salmon_align_quant
starindices
starOutputfiles
transcriptome
Be sure to pay attention to lower and upper case letters and never use a space (don't be a hero, use copy&paste from below)
mkdir AlignedToTranscriptome
mkdir fastqc
mkdir salmon_align_quant
mkdir starindices
mkdir starOutputfiles
mkdir transcriptome
As a habit, list ll what has been set up in your At working directory
ll
You should see all six directories
You may also view them using the tree command to see them nested in your working directory symbolized with a dot .
tree
.
├── AlignedToTranscriptome
├── fastqc
├── salmon_align_quant
├── starindices
├── starOutputfiles
└── transcriptome
Your tree will look like the example above. Remember that your "dot" represents your unique path to your At project space.
/share/bitcpt/Spring2022/UnityID/At
OPTIONAL: If you made any typos or mistakes and need to remove a directory you can use the command to remove directory rmdir however you will not be allowed to use this command once you store anything within the directory.
rmdir ExactNameOfMistake
As a habit, list ls what has been set up or in this case removed from your At working directory
ls
You should see all eight directories minus whatever you deleted.
Remember to go back a step and add the directory properly before moving forward.