Difference between revisions of "INF-BIOX121 H14 RStudio IPython"
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Using the IPython Notebook | Using the IPython Notebook | ||
| + | <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> | ||
| − | + | 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 | ||
| − | + | l<span style="font-size: 12px;">aunch iPython notebook</span> | |
| − | |||
| − | |||
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</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> | ||
| − | < | + | <div><span style="font-size: 12px;">leave both terminal windows open</span><br/></div><div><span style="font-size: 12px;"></span><br/></div> |
| − | < | + | <span style="font-size: 12px;"></span><span style="font-size: 12px;">Windows</span> |
| − | |||
| − | |||
| − | + | <span style="font-size: 12px;">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) | |
| − | <span | + | <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> | ||
| + | Using Rstudio | ||
| − | + | <span style="font-size: 12px;">Linux or Mac</span> | |
| + | open a terminal an write | ||
| + | <span class="s1">ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no</span> | ||
| − | + | <span style="font-size: 12px;">the port number on the left (20000) is an example. Choose any large port number > 20000</span> | |
| − | |||
| + | <span style="font-size: 12px;">the one on the right should *always* be 8787</span> | ||
| + | <span style="font-size: 12px;">Once you type the above command, login with your SSH username and password, like you normally do. </span> | ||
| + | <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><div><br/></div> | ||
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: | 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: | ||
Revision as of 10:44, 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
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.
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.
