Difference between revisions of "INF-BIOX121 H14 RStudio IPython"
From projects/clsi
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=== Using the IPython Notebook === | === Using the IPython Notebook === | ||
| − | *login as usual, with X forwarding on the course server | + | *<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><span style="font-size: 12px;">login as usual, with X forwarding on the course server</span></div> | ||
*start a so-called virtual Python environment (virtualenv): | *start a so-called virtual Python environment (virtualenv): | ||
<pre>source /opt/ipytest/bin/activate</pre> | <pre>source /opt/ipytest/bin/activate</pre> | ||
| Line 10: | Line 11: | ||
*'''Linux''' | *'''Linux''' | ||
**the notebook should start now | **the notebook should start now | ||
| + | **if it doesn't, cancel, close your browser and try again | ||
*'''Mac''' | *'''Mac''' | ||
**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) | **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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<pre>ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no</pre> | <pre>ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no</pre> | ||
*'''<span style="font-size: 12px;">Windows</span>''' | *'''<span style="font-size: 12px;">Windows</span>''' | ||
| − | **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 | + | **<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> |
**source port: 30000 | **source port: 30000 | ||
**destination: [http://127.0.0.1:8888 http://127.0.0.1:8888] (use those same four digits as you noted down above) | **destination: [http://127.0.0.1:8888 http://127.0.0.1:8888] (use those same four digits as you noted down above) | ||
| Line 23: | Line 25: | ||
**point the browser to 127.0.0.1:30000 | **point the browser to 127.0.0.1:30000 | ||
<div><br/></div> | <div><br/></div> | ||
| − | |||
=== Using Rstudio === | === Using Rstudio === | ||
<div><br/></div> | <div><br/></div> | ||
Revision as of 12:52, 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
- Windows
- see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/on how to set up your tunnel
- source port: 30000
- destination: http://127.0.0.1:8888 (use those same four digits as you noted down above)
- 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
- see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/on how to set up your tunnel
- source port: 20000 (choose any large port number > 20000)
- 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
