Difference between revisions of "INF BIOX120 H13 messages"

From projects/clsi
Jump to: navigation, search
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
 +
== Sept. 25, 'tee'  ==
 +
 +
*Advanced unix command-line tip: if you want to save the output of a command to a file instead of sending it to the screen, but still want to follow the output, you can
 +
 +
1) open another terminal window,`cd` to the folder, type
 +
<pre>tail -f outfile.txt</pre>
 +
(use ctrl-C to cancel)
 +
 +
2) pipe through `tee`, which sends output to the screen and a file:
 +
<pre>command infile.txt -parameter 1 -parameter2 |tee output.txt</pre>
 +
<br>
 +
 +
== Sept. 24, Practicals online, IPython  ==
 +
 +
*The most recent version of the assembly practicals, including any corrections made during the module, are found on github here:&nbsp;[https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/tree/master/practicals https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/tree/master/practicals]<br>
 +
*Tip for installing IPython (any platform): use [https://www.enthought.com/products/canopy/ Enthought Canopy] (free academic license) or [https://store.continuum.io/cshop/anaconda/ Anaconda ](free)
 +
 +
== Sept. 20, Evaluation  ==
 +
 +
*We sent around an evaluation form for the first week (up until Thursday). Please fill out!
 +
 +
== Sept. 18, VM use, screen  ==
 +
 +
*The [[VM use|page describing the use of the VM]] from the course room, as well as from home/work is updated, please have a look.
 +
*See this [https://wiki.uio.no/projects/clsi/index.php/Tip:using_screen tip] on running commands that take a long time with `screen`
 +
 +
== Sept. 17, explainshell  ==
 +
 +
*Check out [http://explainshell.com/ http://explainshell.com/]
 +
 
== Sept. 16: Welcome, wiki, messages  ==
 
== Sept. 16: Welcome, wiki, messages  ==
  
Line 4: Line 34:
  
 
*This page can be reached by going to '''bit.ly/htsuio13'''  
 
*This page can be reached by going to '''bit.ly/htsuio13'''  
*the course wiki is at [[INF-BIOX120 H13|here]].
+
*the course wiki is at [[INF-BIOX120 H13|here]].  
 +
*If you do not have a htsXX number, or forgotten which one you used during the unix pre-course, ask the teachers
 +
*loggin into the VM on linux: in a terminal, type&nbsp;
 +
<pre>xfreerdp -k no htsXX.uio.no</pre>
 +
*On the VM, have a look at the /doc folder, it will have the presentation PDF's. Some of them are already uploaded before the actual time of presenting so you can follow along
 +
*SAM flags:&nbsp;http://picard.sourceforge.net/explain-flags.html
 +
*if /data doesnt work, try /site/infbio9120/data. Same for /doc, use &nbsp;/site/infbio9120/doc
  
== Sept. 13th: room ==
+
== Sept. 13th: room ==
  
 
First course day is in Room Cobol at Informatics, [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13#Time_and_place see here].  
 
First course day is in Room Cobol at Informatics, [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13#Time_and_place see here].  
  
 
See you on Monday, September 16th at 9:00!
 
See you on Monday, September 16th at 9:00!

Latest revision as of 10:56, 25 September 2013

Sept. 25, 'tee'

  • Advanced unix command-line tip: if you want to save the output of a command to a file instead of sending it to the screen, but still want to follow the output, you can

1) open another terminal window,`cd` to the folder, type

tail -f outfile.txt

(use ctrl-C to cancel)

2) pipe through `tee`, which sends output to the screen and a file:

command infile.txt -parameter 1 -parameter2 |tee output.txt


Sept. 24, Practicals online, IPython

Sept. 20, Evaluation

  • We sent around an evaluation form for the first week (up until Thursday). Please fill out!

Sept. 18, VM use, screen

  • The page describing the use of the VM from the course room, as well as from home/work is updated, please have a look.
  • See this tip on running commands that take a long time with `screen`

Sept. 17, explainshell

Sept. 16: Welcome, wiki, messages

Welcome!

  • This page can be reached by going to bit.ly/htsuio13
  • the course wiki is at here.
  • If you do not have a htsXX number, or forgotten which one you used during the unix pre-course, ask the teachers
  • loggin into the VM on linux: in a terminal, type 
xfreerdp -k no htsXX.uio.no
  • On the VM, have a look at the /doc folder, it will have the presentation PDF's. Some of them are already uploaded before the actual time of presenting so you can follow along
  • SAM flags: http://picard.sourceforge.net/explain-flags.html
  • if /data doesnt work, try /site/infbio9120/data. Same for /doc, use  /site/infbio9120/doc

Sept. 13th: room

First course day is in Room Cobol at Informatics, see here.

See you on Monday, September 16th at 9:00!