[Bio-Linux] assigning bash variables

[Tim Booth]

Hi Giulia,

Someone has switched your login shell to TCSH (or maybe CSH).  I've
confirmed that when I run those commands under TCSH I get the same
errors as you.

You can set your shell preference back by using the 'chsh' command.
You'll be prompted for the shell to use and you can either go
for /bin/zsh or /bin/bash.  ZSH is the Bio-Linux default as I find it a
more friendly interactive shell when using tab-completion etc. but BASH
is the more usual Linux shell and the default for Ubuntu.  Both are
supported on BL and both will accept variable assignments the way you
are trying (and as Bela noted, both use "export" to turn shell variables
into environment variables).  Log out then in again to get the new
shell.

If for some reason you don't want to run "chsh" on the account just run
"exec zsh" and you'll be in ZSH until you close the terminal.

Cheers,

TIM

On Mon, 2015-02-16 at 14:36 +0000, Bela Tiwari wrote:
> Hello, 
> 
> 
> 
> >I’m using Biolinux 8 on a university PC (I login as user and not
> admin) and I’m having problem with 
> >a very basic task – assigning variables in the shell!
> 
> 
> If you're trying to set environmental variables, you'll need to use
> export before the rest of the statement. 
> 
> e.g.
> 
> 
> export MYVAR=1 
> 
> 
> Setting environmental variables is covered on page 29 of the Bio-Linux
> tutorial:
> 
> 
> 
> http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf
> 
> 
> 
> I hope that's the information you were looking for. 
> 
> 
> 
> Best wishes, 
> 
> 
> 
> Bela
> 
> 
> 
> Den Mandag, 16. februar 2015 12.38 skrev Giulia Zancolli
> <g.zancolli at bangor.ac.uk>:
> 
> 
> 
> Hello,
> I’m using Biolinux 8 on a university PC (I login as user and not
> admin) and I’m having problem with a very basic task – assigning
> variables in the shell!
>  
> I type something very simple like 
>  
> a=1 
>  
> and I get the error: command “a=” not found
> 
> or the following (which was working perfectly in Linux on my laptop)
>  
> LIST="$(ls | grep "fastq$")"
>  
> And I get the error “Illegal variable name”
>  
> What might be wrong?
>  
> Any clue is very appreciated!
>  
> Giulia
>  
> Dr Giulia Zancolli
> Molecular Ecology and Fisheries Genetics Lab
> School of Biological Sciences    
> Bangor University
> Environment Centre Wales
> Bangor LL57 2UW                 
> UK 
>  
>  
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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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