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Old 08-06-2011, 03:27 AM   #1
yifangt
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Location: Canada

Join Date: Feb 2011
Posts: 61
Default Environment setting related to GSL!

Hello!

While I was trying to install the BIOS of RSEQtools package according to the documentation I got confused about the environment settings, which says:
Code:
Step 1: Download BIOS.

Step 2: Other requirements: GNU Scientific Library

Step 3: Set the environment variables:
  - BIOINFOCONFDIR=/pathTo/bios/conf
  - BIOINFOGSLDIR=/pathTo/gsl-X.XX

Step 4: Compiling BIOS:
  make
  make prod

Optional: Doxygen (version 1.5.7.1) is used to document the code.
The following environment variables are required:
- BIOINFODOXYGENBINDIR=/pathTo/doxygen-1.5.7.1/bin
- BIOINFODOXYGENDOCDIR=/pathTo/public_html/bios
- BIOINFOWEBSERVER=webServer.org
My desktop is Ubuntu Natty (11.04) on Linux kernel 2.6.38.11-server with GNOME 2.32.1. I assume both the "GNU Scientific Library" and Doxygen have been installed as I found following packages are there with my synaptic package manager:
Code:
libgsl0-dev  1.14+dfsg-1
libgsloldbl   1.14+dfsg-1
doxygen      1.7.3-6ubuntu
But I could not locate the files in a similar format as gsl-1.14 and /doxygen-1.7.3/bin in the file system when I tried to set the environment variables. My questions are:

1) Do I still need to set the environment variables with my system?
2) For my situation, how do I get the correct environment variables if needed?
3) I assume the environment variables are put in my /etc/bash.bashrc file. Is this correct? If yes, how?

Please forgive me if these questions are too naive as I am beginner. Have asked the author, but no response.

Thank you in advance!

Yifang
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