Difference between revisions of "INF-BIOX121 H14 RStudio IPython"

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=== Using the IPython Notebook ===
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*<div><u>note to Windows users</u>: your best option is to click the 'penguin' icon on the desktop and turn your PC into a Linux machine - then follow the instructions for Linux<br/></div>
 +
*<div>login as usual, with X forwarding on the course server</div>
 +
*start a so-called virtual Python environment (virtualenv):
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<pre>source /opt/ipytest/bin/activate</pre>
 +
*this changes your promt, don't worry.
 +
*move (cd) to a folder if needed, for example where the data is you want to analyse
 +
*launch iPython notebook
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<pre>ipython notebook</pre>
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*'''Linux'''
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**the notebook should start now
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**if it doesn't, cancel, close your browser and try again
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*'''Mac'''
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**check where it says "The IPython Notebook is running at: [http://127.0.0.1:8888/ http://127.0.0.1:8888/]" and note the last four digits ('8888' in this case)
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**start another terminal session and you create a so-called SSH tunnel, make sure to use the same four digits in the middle
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<pre>ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no</pre>
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*'''<span style="font-size: 12px;">​Windows</span>'''
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**<span style="font-size: 12px;">see </span>[http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/]<span style="font-size: 12px;">on how to set up your tunnel</span>
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**source port: 30000
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**destination: [http://127.0.0.1:8888 http://127.0.0.1:8888] (use those same four digits as you noted down above)
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*'''All'''
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**on the classroom PC, open a webbrowser (e.g. firefox)
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**point the browser to 127.0.0.1:30000
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<div><br/></div>
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=== Using Rstudio ===
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<div><br/></div>
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*Linux or Mac
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**open a terminal and write
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<pre>ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no</pre>
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**the port number on the left (20000) is an example. Choose any large port number > 20000
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**the one on the right should *always* be 8787
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**Once you type the above command, login with your SSH username and password, like you normally do. &nbsp;
 +
 
 +
*​Windows
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**see [http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/]on how to set up your tunnel
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**<span style="font-size: 12px;">source port: 20000 (choose any large port number > 20000)</span>
 +
**destination: localhost:8787 (dont change this number)
 +
*All
 +
**on the classroom PC, open a webbrowser (e.g. firefox)
 +
**point the browser to localhost:20000 to access the RStudio server login screen
 +
**you can then type your username and password to login and access your R environment from your web browser
 +
<div><br/></div>

Latest revision as of 11:52, 10 October 2014

Using the IPython Notebook

  • note to Windows users: your best option is to click the 'penguin' icon on the desktop and turn your PC into a Linux machine - then follow the instructions for Linux
  • login as usual, with X forwarding on the course server
  • start a so-called virtual Python environment (virtualenv):
source /opt/ipytest/bin/activate
  • this changes your promt, don't worry.
  • move (cd) to a folder if needed, for example where the data is you want to analyse
  • launch iPython notebook
ipython notebook
  • Linux
    • the notebook should start now
    • if it doesn't, cancel, close your browser and try again
  • Mac
    • check where it says "The IPython Notebook is running at: http://127.0.0.1:8888/" and note the last four digits ('8888' in this case)
    • start another terminal session and you create a so-called SSH tunnel, make sure to use the same four digits in the middle
ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no
  • All
    • on the classroom PC, open a webbrowser (e.g. firefox)
    • point the browser to 127.0.0.1:30000

Using Rstudio


  • Linux or Mac
    • open a terminal and write
ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no
    • the port number on the left (20000) is an example. Choose any large port number > 20000
    • the one on the right should *always* be 8787
    • Once you type the above command, login with your SSH username and password, like you normally do.  
  • ​Windows
  • All
    • on the classroom PC, open a webbrowser (e.g. firefox)
    • point the browser to localhost:20000 to access the RStudio server login screen
    • you can then type your username and password to login and access your R environment from your web browser