[Bioperl-l] Re: Inline::C and io_lib

[Aaron J Mackey]

On Tue, 9 Jul 2002, Lincoln Stein wrote:

> I think that bioperl-ext is the place where other modules that have C-compiler
> requirements go.

OK, seems reasonable.  What I'll do is put Bio/SeqIO/staden/read.pm there
(with it's appropriate Makefile.PL), and put all the SeqIO/abi.pm, etc. in
bioperl-live; they'll each try to load staden::read, and if they can't,
they'll fail gracefully (i.e. throw an exception that instructs the user
to get io_lib and the bioperl-ext package).

> I suggest that Makefile.PL be set up to take command-line arguments so
> that the locations of the INC and LIB directories can be set from
> within a script.

Sure; I've also seen environment variables used this way (csh example):

% setenv IOLIB_INC /opt/include/io_lib
% setenv IOLIB_LIB /opt/lib/
% perl Makefile.PL

Also allowable:

% perl Makefile.PL IOLIB_LIB=/opt/lib IOLIB_INC=/opt/include/io_lib

Does this all sound good?

-Aaron

P.S. I'm using the staden convert_trace utility to generate trace files in
these various formats from Chad's "version3.scf" file in t/data/ - but it
seems to choke for 'abi' and 'alf' formats ... anyone have a file or two
of these formats for me to test with?