Difference between revisions of "INF-BIOX121 H14 RStudio IPython"
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− | *<span style="font-size: 12px;">login as usual, with X forwarding on </span>tjhe course server | + | *<span style="font-size: 12px;">login as usual, with X forwarding on </span>tjhe course server |
*<span style="font-size: 12px;">start a so-called virtual Python environment (virtualenv):</span> | *<span style="font-size: 12px;">start a so-called virtual Python environment (virtualenv):</span> | ||
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ipython notebook | ipython notebook | ||
− | * | + | *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) |
− | *<span style="font-size: 12px;">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</span> | + | *<span style="font-size: 12px;">MAC/Linux</span> |
+ | **<span style="font-size: 12px;">start another terminal session and you create a so-called SSH tunnel, make sure to use the same four digits in the middle</span> | ||
<span style="font-size: 12px;">ssh -L 30000:127.0.0.1:8888 </span><span style="font-size: 12px;">username@bioinfcourse.hpc.uio.no</span> | <span style="font-size: 12px;">ssh -L 30000:127.0.0.1:8888 </span><span style="font-size: 12px;">username@bioinfcourse.hpc.uio.no</span> | ||
+ | <ul style="margin-left: 40px;"> | ||
+ | <li><span style="font-size: 12px;"><div>leave both terminal windows open</div>Windows users: 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> | ||
+ | *source port: 30000 | ||
+ | *destination: 127.0.0.1:8888 (use those same four digits as you noted down above)</li> | ||
− | *<span style="font-size: 12px;"> | + | *<span style="font-size: 12px;">on the classroom PC, open a webbrowser (e.g. firefox)</span> |
− | |||
− | |||
− | |||
*point the browser to<span style="font-size: 12px;"> 127.0.0.1:30000</span> | *point the browser to<span style="font-size: 12px;"> 127.0.0.1:30000</span> | ||
Revision as of 10:33, 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 openWindows users: 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
2)To use that instance, it is essential that you use SSH tunneling for security purposes. From a Linux or Mac workstation/laptop, you can type something like the one below:
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. Once you are in, you can THEN point your LOCAL workstation/laptop browser to the URL: 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.
3)For Windows users, you should use an SSH client like PuTTY. You can then establish a tunnel in a similar way as step 2) above by using this document as a guide:
http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/