Strangled by IPython

Today we started grappling with terminal and IPython to try BLASTing…

It was quite a learning experience, trying to understand how a computer “thinks” to do what we want it do (along with bioinformatics techniques).

Before we went to IPython, we started with terminal, in which we set up our directories in Maxene.  Our process:

  1. say i love terminal – made our computer say “I love terminal”
  2. say please don’t fail me – made our computer beg for mercy
  3. pwd – present working directory, shows what directory we’re in at the time
  4. cd /Applications/blast – change our directory to the blast folder in applications
  5. ls – list, shows what’s in the current directory
  6. mkdir DB – make a database called “DB” OH NO!  We need admin permissions -_____-
  7. So… cd ../ to move up through directories
  8. Then move down directories… cd Users and so forth until we reach our needed folders in maxene
  9. In my own folder in our classes, mkdir DB to make the database DB!  Yay!
  10. Now ipython notebook to get whisked off to IPython


Sadly, my IPython is not working with me and isn’t exporting an html properly so this will be updated as soon as that’s figured out…

In all honesty, today was pretty fun and I’m stoked to try using IPython to execute R statistics.  A new day tomorrow!

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