• bshaban
  1. Spartan Course Content

    Spartan workshop content:   https://github.com/UoM-ResPlat-DevOps/SpartanIntro https://github.com/UoM-ResPlat-DevOps/SpartanAdvanced https://github.com/UoM-ResPlat-DevOps/SpartanRegEx


  2. How to rename fastq headers i.e. remove duplicates

        [bobbieshaban@spartan-login1 analysis]$ cat hiseq_reads_R1.fastq | awk ‘{if(NR%4==1) $0=sprintf(“@1_%d”,(1+i++)); print;}’ | less [bobbieshaban@spartan-login1 analysis]$ cat hiseq_reads_R1.fastq | awk ‘{if(NR%4==1) $0=sprintf(“@1_%d”,(1+i++)); print;}’ > hiseq_R1.fastq [bobbieshaban@spartan-login1 analysis]$ …


  3. WDL/CWL Basics Tutorial – Parkville Data Management and Workflow Group

    Video recordings and slides from WDL/CWL presentation. WDL presentation video: https://www.youtube.com/watch?v=Qw67QU_dUV4&t=44s WDL Slides: WDL  


  4. SumHer Workshop – How to install VirtualBox for Windows

      Instructions for installing VirtualBox on Windows and accessing the SumHer Ubuntu Virtual Machine can be downloaded here: Oracle virtual box – win instructions You can download …


  5. Tutorial 9 – Git basics tutorial

    This tutorial will show the basics of Git. It will go through creating an account, creating a new repo, how to create a branch and how …


  6. Tutorial 7 – HPC- Refresher 05/04/2018

    Tutorial 6 – HPC Refresher Tutorial notes and files for hpc refresher Tutorial7-HPC-Refresher SRR_1.zip Please unzip file SRR_1.zip before using in this tutorial. The video recording …


  7. Tutorial 5 – 09/11/17 – Unix Commands

    Tutorial 5 – More unix commands Please download the following material. tute5.txt tute5.txt is not an actual text file, it is a tar. Please download, rename …


  8. Tutorial 4 – Linux command line 26/10/17

    This tutorial will go through some examples of some linux command line tools. Please download the tutorial notes and these files and place in a directory …


  9. Installing R packages locally

    Installing R packages locally. Create .Revniron in your home directory Create directory /vlsci/SG000x/shared/rlibs/ – where x is your group id Add the following lines – change …


  10. Tutorial 3 – Virtual box installation – 12/10/17

    This week’s tutorial will consist of installing Virtual Box and installing a virtual machine. This tutorial will be the prelude to further tutorials where we will …


Number of posts found: 27