Page Comparison

Test

Before we start using the HPC, let’s start an interactive session:

qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=1:mem=4gb

Get a copy of the scripts to be used in this module

Use the terminal to log into the HPC and create a /RNAseq/ folder to run the nf-core/rnaseq pipeline. For example:

mkdir -p $HOME/workshop/2024/rnaseq/scripts
cp /work/training/2024/rnaseq/scripts/* $HOME/workshop/2024/rnaseq/scripts/
ls -l $HOME/workshop/2024/rnaseq/scripts/

• Line 1: The -p indicates create 'parental directories as required. Thus the line 1 command creates both /workshop/ and the subfolder /workshop/scripts/

• Line 2: Copies all files from /work/datasets/workshop/scripts/ as noted by an asterisk to the newly created folder $HOME/workshop/scripts/

Copy public data to your $HOME

mkdir -p $HOME/workshop/2024/rnaseq/data
cp /work/training/2024/rnaseq/data/* $HOME/workshop/2024/rnaseq/data/
# list the content of the $HOME/workshop/2024/rnaseq/data/ 

• Line 1: The first command creates the folder /scripts/

• Line 2: Copies all files from /work/datasets/workshop/scripts/ folder as noted by an asterisk to newly created $HOME/workshop/scripts/ folder

• Line 3: a quick challenge - see the previous section for hints

Create a folder for running the nf-RNA-seq pipeline

Let’s create an “runs” folder in the ~/workshop/2024/rnaseq folder to run the nf-core/rnaseq pipeline. For example:

mkdir -p $HOME/workshop/2024/rnaseq/runs
mkdir $HOME/workshop/2024/rnaseq/runs/run1_test
mkdir $HOME/workshop/2024/rnaseq/runs/run2_QC
mkdir $HOME/workshop/2024/rnaseq/runs/run3_RNAseq
cd $HOME/workshop/2024/rnaseq/runs

• Lines 1-4: create sub-folders for each exercise

• Line 5: change the directory to the folder “run1_test”

• Line 6: print the current working directory