[Bioperl-l] OS X installation instructions

[Steven Cannon]

> Wow. Thanks Steven for putting that document together. The next time I 
> get a chance to do a refresh on the bioperl website I'll make sure to 
> add it in. Once we have it up on bioperl.org I'll make sure that the 
> appropriate files in bioperl-live mention it.
>
> -chris

Thanks -- hope it will be useful.

In writing these instructions, I did come across a probable bug and a 
fix (quoting from the my instructions):

	... the retrieve_blast.pl script in the 0.9.0 distribution doesn't 
work for me without
	another change -- perhaps made necessary by a change in BLAST 
"request ID"
	format. I changed the first line below to the second:
	
		if($data =~ /RID" VALUE="(\S+)"/s) {
		if($data =~ /RID = (\d+-\d+-\d+)/s) {
	

Also, I think the Bioperl Readme instructions might be clarified in the 
"Bioperl XS extentions" section (again, quoting from my notes):

	The installation instructions in the Readme files for Bioperl-0.7.2 
and 0.9.0
	are quite confusing, I think, because they describe a 
Compile/SW/libs directory
	which is not in these distributions. You need to download this 
material from
	ftp://bioperl.org/pub/DIST or  ftp://bioperl.org/pub/external/

This might not confuse other folks, but it I ended up spending a while 
poking about the distribution for the Compile/SW/libs directory. It 
would help to add a sentence about downloading this directory, before 
"Move to the directory Compile/SW" or "You should add the line -fPIC to 
the CFLAGS line in Compile/SW/libs/makefile."

Steve Cannon