[Bioperl-l] Installing bioperl-ext-1.4

[Guillaume Rousse]

bcur001 at ec.auckland.ac.nz wrote:
> I am wanting to run code to do smith-waterman alignment. From what I can see, I
> need the EMBOSS suite, which appears to come as part of bioperl-ext-1.4.
> 
> I have installed bioperl-1.4 fine. when I attempt to install bioperl-ext-1.4
> however, I encounter problems. I've worked my way through a few initial errors,
> finding and installing the staden library and the Inline pm (both of which
> appear to ahve installed fine), I have, however, finally been stumped. Upon
> attempting to run `perl Makefile.PL` from the bioperl-ext-1.4/ directory, I get
> the following:
> 
> Writing Makefile for Bio::Ext::Align
> Found Staden io_lib "libread" in /usr/local/lib ...
> Automatically using the Read.h found in /usr/local/include/io_lib ...
> Writing Makefile for Bio::SeqIO::staden::read
> Writing Makefile for Bio
> One or more DATA sections were not processed by Inline.
Sorry, I missed this post.

Unless you have really good reasons to do so, you'd better use official 
contrib packages for EMBOSS, io_lib and bioperl (I'm the maintainer) 
instead of attempting manual installs. EMBOSS is installed with better 
defaults as by default installation script, io_lib is patched for wrong 
headers, and Bioperl has every needed dependencies packaged. Only 
bioperl-ext is missing, because I never succedeed building it due to 
problem in Makemaker::Inline.

Just try:
urpmi emboss perl-Bioperl-Run libio_lib1-devel

To have everything installed with needed dependancies.

(forget my initial private mail, it was send too early)
-- 
A bad dinner with your wife is worth more than a good one in the company 
of your mother-in-law.
		-- A law for married men