Chado Environment Variable issue

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Chado Environment Variable issue

Shane McCoy
Hello! 
Having issue w/ my environment variable during 'perl Makefile.PL' for Chado install. 

bjreadin@nc:~/trunk/chado$ perl Makefile.PL

************************************************************************

The following enviroment variables not detected:

  CHADO_DB_NAME

Please read the INSTALL document and set required environment variables.

************************************************************************


I have this in my .bashrc 

GMOD_ROOT=/home/bjreadin/trunk/chado

CHADO_DB_NAME=sbass_ncsu

CHADO_DB_USERNAME=bjreadin



plus psql -l >>> sbass_ncsu | bjreadin | UTF8     | en_US.UTF-8 | en_US.UTF-8 | 


any thoughts would be great!

thanks!

Shane M.


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Re: Chado Environment Variable issue

Karl O. Pinc
On 11/26/2014 02:17:41 PM, Shane McCoy wrote:
> Hello!
> Having issue w/ my environment variable during 'perl Makefile.PL' for
> Chado
> install.

> I have this in my .bashrc
>
> GMOD_ROOT=/home/bjreadin/trunk/chado
>
> CHADO_DB_NAME=sbass_ncsu
>
> CHADO_DB_USERNAME=bjreadin
>
>
>
> plus psql -l >>> sbass_ncsu | bjreadin | UTF8     | en_US.UTF-8 |
> en_US.UTF-8 |
>
>
> any thoughts would be great!

You probably want:

export GMOD_ROOT=/home/bjreadin/trunk/chado

(etc.)

Without the "export" child processes, like perl, won't
see the variable.


You probably also want to put them in
.bash_profile instead of .bashrc.  This sets them
up when you login, not whenever bash is invoked.

There's no point in re-executing if you run
some shell program.

(However, if you invoke bash via, e.g,, cron
you will then need to make sure the env vars
are properly setup.  Likely, you'd invoke
perl or whatever directly, in which case
you need to set up the env vars from within,
say, cron, anyway.)


FWIW, I had a very hard time installing chado
from the shell.  I can send you my (cryptic)
notes offlist if you like.

Regards,

Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: Chado Environment Variable issue

Shane McCoy
You were correct in the export missing. 
Thanks Karl! 

On Wed, Nov 26, 2014 at 3:24 PM, Karl O. Pinc <[hidden email]> wrote:
On 11/26/2014 02:17:41 PM, Shane McCoy wrote:
> Hello!
> Having issue w/ my environment variable during 'perl Makefile.PL' for
> Chado
> install.

> I have this in my .bashrc
>
> GMOD_ROOT=/home/bjreadin/trunk/chado
>
> CHADO_DB_NAME=sbass_ncsu
>
> CHADO_DB_USERNAME=bjreadin
>
>
>
> plus psql -l >>> sbass_ncsu | bjreadin | UTF8     | en_US.UTF-8 |
> en_US.UTF-8 |
>
>
> any thoughts would be great!

You probably want:

export GMOD_ROOT=/home/bjreadin/trunk/chado

(etc.)

Without the "export" child processes, like perl, won't
see the variable.


You probably also want to put them in
.bash_profile instead of .bashrc.  This sets them
up when you login, not whenever bash is invoked.

There's no point in re-executing if you run
some shell program.

(However, if you invoke bash via, e.g,, cron
you will then need to make sure the env vars
are properly setup.  Likely, you'd invoke
perl or whatever directly, in which case
you need to set up the env vars from within,
say, cron, anyway.)


FWIW, I had a very hard time installing chado
from the shell.  I can send you my (cryptic)
notes offlist if you like.

Regards,

Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein


------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
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