Difference between revisions of "INF-BIOX121 H14 RStudio IPython"
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| − | + | Using the IPython Notebook | |
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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;"></span> | ||
| + | *<span style="font-size: 12px;">start a so-called virtual Python environment (virtualenv):</span> | ||
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| + | source /opt/ipytest/bin/activate | ||
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| + | *this changes your promt, don't worry. | ||
| + | *move (cd) to a folder if needed, for example where the data is you want to analyse | ||
| + | *l<span style="font-size: 12px;">aunch iPython notebook</span> | ||
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| + | ipython notebook | ||
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| + | *<span style="font-size: 12px;"></span>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) | ||
| + | *<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> | ||
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| + | <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> | ||
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| + | *<span style="font-size: 12px;"></span><span style="font-size: 12px;">Windows users: see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel</span> | ||
| + | *<span style="font-size: 12px;"></span> | ||
| + | *leave both terminal windows open | ||
| + | *on the classroom PC, open a webbrowser (e.g. firefox) | ||
| + | *point the browser to<span style="font-size: 12px;"> 127.0.0.1:30000</span> | ||
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| + | Using Rstudio | ||
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| + | <span style="font-size: 12px;">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:</span> | ||
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| + | <span class="s1">ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no</span> | ||
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| + | (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) | ||
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| + | 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. | ||
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| + | 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: | ||
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| + | <span class="s2">[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> | ||
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| + | For any issues/help, feel free to communicate with me directly. | ||
Revision as of 10:27, 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
- Windows users: see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel
- leave both terminal windows open
- 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/
For any issues/help, feel free to communicate with me directly.
