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7 messages · Elham -, Sarah Goslee, John McKown +1 more

Original
Elham -
# 
hi all,?I am following?http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/?I need to download phenotypic data in the form of text file that describe chip names, and the source of the biological samples as well as probe that hybridised to them. I can not understand the mean of "Open a new terminal window and type".
i am using command.$ ls data/*.CEL > data/phenodata.txt in R

this returns an error


$ ls data/*.CEL > data/phenodata.txt Error: unexpected '$' in "$"
what should I do now?
Sarah Goslee
# 
This isn't an R question, but a linux question.

Open a new terminal window:
The directions you are following tell you how to do that for the
Ubuntu linux being used, right at the beginning:

Open up a terminal (Applications->Accessories->Terminal from the the toolbar)

As for your command, the $ is a prompt. You don't type that. Start with ls

What should you do now? Read a little bit about using linux command line tools

Sarah



On Fri, Dec 30, 2016 at 12:57 PM, Elham - via R-help
<r-help at r-project.org> wrote:
John McKown
# 
On Fri, Dec 30, 2016 at 12:08 PM, Sarah Goslee <sarah.goslee at gmail.com>
wrote:
?Well, this being the R language forum, perhaps you should enter "R" after
the command prompt?

Seriously, what do you want to accomplish? Since you are using Ubuntu, I
will assume that you are using the default shell program, BASH. There is a
BASH forum you could join called mailto:help-bash at gnu.org . It's easiest to
sign up here:
https://lists.gnu.org/mailman/listinfo/help-bash
This site has some nice articles about BASH and programming (scripting)
using it: http://wiki.bash-hackers.org/
BASH for beginners: http://www.tldp.org/LDP/Bash-Beginners-Guide/html/
Since you seem to be using Ubuntu:
https://help.ubuntu.com/community/Beginners/BashScripting

There are _TONS_ of commands installed in Ubuntu by default. Most of them
have manual (man) pages. Most of the defaults are in the directory
/usr/bin. You can list them simply by entering the command: "ls /usr/bin".
My system has over 6,500 programs stuffed in there. If you see something
interesting, you can get some basic documentation on it by using the
command: "man <cmd-name>". We've mentioned "ls", which lists the contents
of a directory. If you want to know more, try "man ls". In addition to
"man" there is a much more powerful information source called "info". Just
use it instead of "man" as the command name. That is, use "info ls" to get
some real detailed information on the ls command.

Another interesting command is "apropos". Think of it as being similar to
the R systems' double question mark search. As an example, suppose you want
to find out what commands might be helpful with a "zip" file. Enter the
command: "apropos zip". On my system, I get a (truncated) response such as:

bunzip2 (1)          - a block-sorting file compressor, v1.0.6
bzip2 (1)            - a block-sorting file compressor, v1.0.6
bzip2recover (1)     - recovers data from damaged bzip2 files
bzless (1)           - file perusal filter for crt viewing of bzip2
compressed text
decode (n)           - Access to zip archives
encode (n)           - Generation of zip archives
funzip (1)           - filter for extracting from a ZIP archive in a pipe
gunzip (1)           - compress or expand files
gzip (1)             - compress or expand files
IO::Compress::Bzip2 (3pm) - Write bzip2 files/buffers
IO::Compress::Zip (3pm) - Write zip files/buffers
IO::Uncompress::Unzip (3pm) - Read zip files/buffers
unzip (1)            - list, test and extract compressed files in a ZIP
archive
unzipsfx (1)         - self-extracting stub for prepending to ZIP archives
zforce (1)           - force a '.gz' extension on all gzip files
zip (1)              - package and compress (archive) files
zipcloak (1)         - encrypt entries in a zipfile

Note the number in the parentheses after the command. A "1" indicates this
is a normal command. Something which starts with a "3" (like 3pm) means
this is like a subroutine package (The "pm" in 3pm means "Perl Module" -
like an R package, sort of). Also note that some of the entries have
nothing to do with a normal "zip" file; such as the entires with bzip2 in
them - bzip2 is an alternative compressor program).

I'm fairly good with BASH, having programmed for over 3 decades, and used
BASH for about 10 years. Which is both good and bad. The good is that I
understand BASH fairly well. The bad is that I like "tricky coding" (a
personal problem).
Elham -
# 
actually I do not work with linux. do you know same of this tutorial for windows?
On Friday, December 30, 2016 10:16 PM, John McKown <john.archie.mckown at gmail.com> wrote:

        
On Fri, Dec 30, 2016 at 12:08 PM, Sarah Goslee <sarah.goslee at gmail.com> wrote:

        
This isn't an R question, but a linux question.

Open a new terminal window:
The directions you are following tell you how to do that for the
Ubuntu linux being used, right at the beginning:

Open up a terminal (Applications->Accessories-> Terminal from the the toolbar)

As for your command, the $ is a prompt. You don't type that. Start with ls

What should you do now? Read a little bit about using linux command line tools


?Well, this being the R language forum, perhaps you should enter "R" after the command prompt?
Seriously, what do you want to accomplish? Since you are using Ubuntu, I will assume that you are using the default shell program, BASH. There is a BASH forum you could join called mailto:help-bash at gnu.org . It's easiest to sign up here:?https://lists.gnu.org/mailman/listinfo/help-bashThis site has some nice articles about BASH and programming (scripting) using it:?http://wiki.bash-hackers.org/BASH for beginners:?http://www.tldp.org/LDP/Bash-Beginners-Guide/html/Since you seem to be using Ubuntu:?https://help.ubuntu.com/community/Beginners/BashScripting
There are _TONS_ of commands installed in Ubuntu by default. Most of them have manual (man) pages. Most of the defaults are in the directory /usr/bin. You can list them simply by entering the command: "ls /usr/bin". My system has over 6,500 programs stuffed in there. If you see something interesting, you can get some basic documentation on it by using the command: "man <cmd-name>". We've mentioned "ls", which lists the contents of a directory. If you want to know more, try "man ls". In addition to "man" there is a much more powerful information source called "info". Just use it instead of "man" as the command name. That is, use "info ls" to get some real detailed information on the ls command.
Another interesting command is "apropos". Think of it as being similar to the R systems' double question mark search. As an example, suppose you want to find out what commands might be helpful with a "zip" file. Enter the command: "apropos zip". On my system, I get a (truncated) response such as:
bunzip2 (1) ? ? ? ? ?- a block-sorting file compressor, v1.0.6bzip2 (1) ? ? ? ? ? ?- a block-sorting file compressor, v1.0.6
bzip2recover (1) ? ? - recovers data from damaged bzip2 filesbzless (1) ? ? ? ? ? - file perusal filter for crt viewing of bzip2 compressed textdecode (n) ? ? ? ? ? - Access to zip archives
encode (n) ? ? ? ? ? - Generation of zip archives
funzip (1) ? ? ? ? ? - filter for extracting from a ZIP archive in a pipegunzip (1) ? ? ? ? ? - compress or expand files
gzip (1) ? ? ? ? ? ? - compress or expand filesIO::Compress::Bzip2 (3pm) - Write bzip2 files/buffers
IO::Compress::Zip (3pm) - Write zip files/buffers
IO::Uncompress::Unzip (3pm) - Read zip files/buffers
unzip (1) ? ? ? ? ? ?- list, test and extract compressed files in a ZIP archive
unzipsfx (1) ? ? ? ? - self-extracting stub for prepending to ZIP archiveszforce (1) ? ? ? ? ? - force a '.gz' extension on all gzip fileszip (1) ? ? ? ? ? ? ?- package and compress (archive) fileszipcloak (1) ? ? ? ? - encrypt entries in a zipfile
Note the number in the parentheses after the command. A "1" indicates this is a normal command. Something which starts with a "3" (like 3pm) means this is like a subroutine package (The "pm" in 3pm means "Perl Module" - like an R package, sort of). Also note that some of the entries have nothing to do with a normal "zip" file; such as the entires with bzip2 in them - bzip2 is an alternative compressor program).

I'm fairly good with BASH, having programmed for over 3 decades, and used BASH for about 10 years. Which is both good and bad. The good is that I understand BASH fairly well. The bad is that I like "tricky coding" (a personal problem).
?

Sarah

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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That page was designed by and for someone with  Linux installation. To quote from the opening paragraph: "Some familiarity with Linux is ideal and the instructions were developed on Ubuntu 11.04, R 2.12.1. For a full code listing for this tutorial and figures resulting from it see the second part of the article."

            

      
      
      
    

        
It later runs out that you are on Windows?  .... ???

            

      
      
      
    

        
There is a help facility for BioC questions. (I think it might now  be web-based unlike this mailing list which remains plain text.)  I suggest you read the Posting Guide more thoroughly that it appears you have so far.

        

      
      
    

        
David Winsemius
Alameda, CA, USA

  
  


  


      

    

    

      
      

        


  

        

      Elham -
    

    

      
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yes me too,but I do not have time to install and learn linux,I need tutorial based on windows

        
On Saturday, December 31, 2016 3:50 AM, David Winsemius <dwinsemius at comcast.net> wrote:

        

            

      
      
      
    

        
That page was designed by and for someone with? Linux installation. To quote from the opening paragraph: "Some familiarity with Linux is ideal and the instructions were developed on Ubuntu 11.04, R 2.12.1. For a full code listing for this tutorial and figures resulting from it see the second part of the article."

            

      
      
      
    

        
It later runs out that you are on Windows?? .... ???

            

      
      
      
    

        
There is a help facility for BioC questions. (I think it might now? be web-based unlike this mailing list which remains plain text.)? I suggest you read the Posting Guide more thoroughly that it appears you have so far.

        

      
      
    

        
David Winsemius
Alameda, CA, USA

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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Fine. But you are asking in the wrong place. It's a BioC question. Most of us here are not Bioc users. Use the forum that is designed for that purpose.