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Intro to Unix

Commands

You'll want to find some Unix cheat sheet on google.

ls  # -a -l -t -h)
pwd
cd  # dir .. ~ 
mkdir
nano 
mv
cp
ln 
rm
rmdir
wget  # download file (first)
head
tail
less
grep 
getting help; running stuff
R

Examples

  • example: run blast of gene against swissprot http://www.antgenomes.org/~yannickwurm/tmp/2014-10-15-Swissprot.zip

  • example: seqtk compile ; extract scaffold00059

Resource monitoring

  • htop or top
  • who
  • finger

Shared computing - HPC concept

Remote:

Practical

Thanks to Amazon Web Services for providing free access for this course (grant EDU_E_FY2014_Q4_QueenMaryULondon_Wurm).

Unix

  1. Use MobaXterm (on Windows) or Terminal to: ssh [email protected] secret: ____arethebest
  2. In the home folder, create your own directory (subfolder) with your name.
  3. Within this directory, launch R - make a plot.
  4. Within this new directory, download a fasta sequence, BLAST it against Swissprot - monitor with htop (in a different window) while this happens.
  5. Download a genome sequence, use seqtk to extract a specific sequence

Gene annotation

http://afra.sbcs.qmul.ac.uk