[Bio-Linux] Bio-Linux5 local documentation

[Tony Travis]

Hello, Stewart.

The local documentation for EMBOSS is broken. For example, the link for 
"abiview" is:

file:///usr/local/bioinf/documentation/EMBOSS/doc/programs/html/abiview.html

This file does not exist...

A simple work-around is:

cd /usr/local/bioinf/documentation
ln -s /usr/local/bioinf/EMBOSS/EMBOSS-6.0.1/emboss/share/EMBOSS .

I think that using 'file' URL's is bad, because they break when you 
access Bio-Linux documentation using an external web browser. I posted 
this 'fix' to make the documentation URL's relative to the webserver's 
document root under 'biobuntu' (Bio-Linux4 + Ubuntu 6.06) on the NBX:

----- cut here -----
#!/bin/sh
# @(#)fix_bioinfo.sh  2007-09-28  A.J.Travis
#
# Fix file:/// URL's in Bio-Linux documentation
#
cd /var/www/bioinformatics/docs
ln -s /usr/local/bioinf/documentation .
for i in *.html; do
ed $i <<End
1,\$s/file:\/\/\/usr\/local\/bioinf\///
w
q
End
done
----- cut here -----

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt