[Bio-linux-dev] bash compatibility

[Tim Booth]

Hi Tony,

Perhaps you could weigh in on this discussion?

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=776663

Note the comment from Axel Beckert:

"With respect to shells, I usually find that applications, that need to
inject code into a user's shell to be by and large mis-designed."

I actually agree.  Applications should not rely on the behaviour of the
controlling shell.  My reason for making the wishlist request was to
allow Andreas' proposed blend selection system to function outside of
Bash, and that's an issue related to default preferences rather than a
requirement for functionality.

Cheers,

TIM

On Tue, 2015-02-03 at 20:06 +0000, Tony Travis wrote:
> Hi, Tim.
> 
> There is a problem with bash compatibility in Bio-Linux 8 because "zsh"
> does NOT source /etc/profile by default. Here's a patch to do it:
> 
> --- old/zprofile	2013-08-02 22:29:03.000000000 +0530
> +++ zprofile	2015-02-04 01:14:06.747837184 +0530
> @@ -5,3 +5,6 @@
>  # shells invoked with the -l flag.)
>  #
>  # Global Order: zshenv, zprofile, zshrc, zlogin
> +
> +# for compatibility with "bash"
> +emulate sh -c 'source /etc/profile'
> 
> In particular, "profile" fragments installed by packages (or manually)
> are never sourced from /etc/profile.d by "zsh" and this breaks things
> quite badly on our servers. I didn't notice this previously because we
> don't use "zsh". However, the servers at Assam Agricultural University
> are set up to use "zsh" for the course, so we can follow your tutorial.
> 
> We are installing our own GWAS pipeline called "ParSNP" that uses
> /etc/profile.d to set the environment in the normal way for "bash".
> 
> Bye,
> 
>   Tony.
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
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