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Overview:
Create working directory folders for hands-on training exercises
Copy data and scripts for today’s session
(Optional - those that did not attend Session 3) run a test to verify Nextflow is properly installed and to test the execution of the nf-core/rnaseq pipeline with example data provided by developers.
Prepare Working Directory Space for Session 4 |
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Before we start using the HPC, let’s start an interactive session:
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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
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where:
‘walltime’ is amount of time requested to run the interactive session
‘cpus’ number of CPUs to be used by the interactive session
‘mem’ amount of memory assigned to the interactive session
Create working directories
Let’s create the working directories for today’s session:
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mkdir -p$HOME/workshop/2024-2/session4_RNAseq mkdir $HOME/workshop/2024/rnaseqsession4_RNAseq/scripts cpmkdir $HOME/workworkshop/training/2024/rnaseq/scripts/*session4_RNAseq/data mkdir $HOME/workshop/session4_RNAseq/runs mkdir $HOME/workshop/2024/rnaseq/scripts/ ls -l $HOME/workshop/2024/rnaseq/scripts/ |
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Line 1: The -p indicates create 'parental directories as required. Thus the line 1 command creates both /workshop/ and the subfolder /workshop/scripts/
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/session4_RNAseq/runs/run1_QC
mkdir $HOME/workshop/session4_RNAseq/runs/run2_RNAseq
mkdir $HOME/workshop/session4_RNAseq/runs/run3_RNAseq_T2T |
The folder structure will look like this:
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session4_RNAseq/
├── data
├── runs
│ ├── run1_QC
│ ├── run2_RNAseq
│ └── run3_RNAseq_T2T
└── scripts |
Get a copy of the scripts
Now let’s copy the scripts necessary for today’s session:
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cp /work/training/2024/rnaseq/scripts/* $HOME/workshop/2024-2/session4_RNAseq/scripts |
Line 1: Copies all files from /work/datasets/workshop/scripts/ as noted by an asterisk to the newly created folder $HOME/workshop/2024-2/session4_RNAseq/scripts/
Copy public data to your $HOME
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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/ -2/session4_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 folder $HOME/workshop/scripts/ folderLine 3: a quick challenge - see the previous section for hints2024-2/session4_RNAseq/data/
Using the usage and parameters sections, search how many aligner options are available for the nf-core rnaseq pipeline version 3.15.1.
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ls |
Create a folder for running the nf-RNA-seq pipeline
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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