Difference between revisions of "INF-BIOX121 H14 RStudio IPython"
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| − | Using the IPython Notebook | + | <div>Using the IPython Notebook</div><div><br/></div> |
| − | + | *login as usual, with X forwarding on tjhe course server | |
| − | < | + | *start a so-called virtual Python environment (virtualenv): |
| − | + | <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 | |
| − | source /opt/ipytest/bin/activate | + | *launch iPython notebook |
| − | + | <pre>ipython notebook</pre> | |
| − | this changes your promt, don't worry. | + | *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) |
| − | + | *Mac/Linux | |
| − | move (cd) to a folder if needed, for example where the data is you want to analyse | + | *start another terminal session and you create a so-called SSH tunnel, make sure to use the same four digits in the middle |
| − | + | <pre>ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no</pre> | |
| − | + | *leave both terminal windows open | |
| − | + | *<span style="font-size: 12px;">Windows</span> | |
| − | + | *see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel | |
| − | + | *source port: 30000 | |
| − | check where it says "The IPython Notebook is running at: | + | *destination: 127.0.0.1:8888 (use those same four digits as you noted down above) |
| − | + | *on the classroom PC, open a webbrowser (e.g. firefox) | |
| − | + | *point the browser to 127.0.0.1:30000 | |
| − | + | <div><br/></div><div>Using Rstudio</div><div><br/></div><div>Linux or Mac</div><div>open a terminal an write</div><div>ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no</div><div>the port number on the left (20000) is an example. Choose any large port number > 20000</div><div>the one on the right should *always* be 8787</div><div>Once you type the above command, login with your SSH username and password, like you normally do. </div><div>Windows</div><div><br/></div><div>see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel</div><div><br/></div><div>source port: 20000 (choose any large port number > 20000)</div><div><br/></div><div>destination: localhost:8787 (dont change this number)</div><div><br/></div><div>on the classroom PC, open a webbrowser (e.g. firefox)</div><div><br/></div><div>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><div><br/></div> | |
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| − | source port: 30000 | ||
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| − | destination: 127.0.0.1:8888 (use those same four digits as you noted down above) | ||
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| − | point the browser to | ||
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| − | Using Rstudio | ||
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| − | open a terminal an write | ||
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| − | <div>Windows</div><div><br/></div><div>see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel</div><div><br/></div><div>source port: 20000 (choose any large port number > 20000)</div><div><br/></div><div>destination: localhost:8787 (dont change this number)</div><div><br/></div><div>on the classroom PC, open a webbrowser (e.g. firefox)</div><div><br/></div><div>point the browser to localhost:20000 | ||
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Revision as of 10:46, 8 October 2014
Using the IPython Notebook
- login as usual, with X forwarding on tjhe 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
- 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)
- Mac/Linux
- 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
- leave both terminal windows open
- 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: 127.0.0.1:8888 (use those same four digits as you noted down above)
- 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 an 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)
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.
