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XS-based BioPerl extensions to C libraries (defunct)

markdown-ize README

latest commit 1b597252f6
Chris Fields authored

README.md

Summary

This is the BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions.

These currently include:

Overall notes

This collection of modules is fairly old and no longer actively maintained.

Installing

Depending on your choise of extensions, you might need Inline::MakeMaker and Inline::Cto create the makefile. Use for example the cpan program to install Inline::MakeMaker and answer yes when prompted to install Inline::C.

To install all of the extension packages, you can use the top-level Makefile.PL (present in the same directory you're reading this README from) (Make sure you read the various notes below about each package before doing this!):

perl Makefile.PL
make
make test
make install (may need root permissions)

To install only the individual extensions you wish to have, change directories into each and use the Makefile.PL found there; for example:

cd Bio/Ext/Align
perl Makefile.PL
make
make test (should print out alignment on STDERR)
make install (probably need root permissions).

Notes for Bio::Ext::Align

Although these extensions can be called by themselves, they really need the main bioperl distribution to drive them. The modules which do this are

  • Bio::Tools::pSW - makes Smith-Waterman alignments for DNA
  • Bio::Tools::dpAlign - makes Smith-Waterman alignments for proteins
  • Bio::SearchDist - deals with EVD fitting of extreme value distributions

For more information on how to use these modules, read their own documentation (perldoc Bio::Tools::pSW)

Notes for Bio::SeqIO::staden::read

This extension needs the rest of the main bioperl distribution to function properly. It is only useful as a helper module for the SeqIO system to read sequence trace files handled by the Staden package's io_lib "read" library. You should have this library installed prior to installing Bio::SeqIO::staden::read, it's currently available at:

https://sourceforge.net/project/showfiles.php?group_id=100316

Currently, the Bio::SeqIO::staden::read extension only works with io_lib v. 1.8.11 or 1.8.12; v. 1.9 and higher have several prototype changes in the read library which have broken compatibility in those versions for now. It is possible these changes may be addressed in the future.

Many users have noted that the io_lib install process often forgets to install the os.h file along with the rest of the include files; you may have to do this manually. If so, you may also have to install the config.h file for os.h to find all the information it needs. Finally, you may also need to edit os.h to #include <config.h> instead of #include "config.h" if you continue to get undefined symbol errors during compilation. On some OSes you may in fact have to do the OPPOSITE, meaning change <config.h> to "config.h".

The bioperl-ext make process will prompt you for the LIB and INCLUDE locations (usually /usr/local/lib and /usr/local/include/io_lib, respectively) of the io_lib libread library and Read.h header files, after trying to automatically find them. You may also specify these via the environment variables IOLIB_LIB and IOLIB_INC, or via identically named options to perl Makefile.PL:

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

Ignore any warnings about these options being unknown to MakeMaker.

A failed compilation is most likely due to an incomplete io_lib installation; make sure that all the required io_lib .h files are in place (see above regarding os.h and config.h).

Additional problems may occur that have been associated with the VERSION number that Inline::C uses. Normally, this pops up as an Inline error:

------------------------------------------------------------------------
The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
 '/usr/lib/perl5/site_perl/5.8.0'

If this is a CPAN/distributed module, you may need to reinstall it on your
system.

To allow Inline to compile the module in a temporary cache, simply remove the
Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
------------------------------------------------------------------------

To get around this, either quote out or remove the indicated line from your local Bio/SeqIO/staden/read.pm file after installation:

use Inline (C => 'DATA',
           VERSION => '1.51', # <--- this line
           NAME => 'Bio::SeqIO::staden::read',
           LIBS => "-L/usr/local/lib -lread -lz", # leave these as double quotes - necessary for Makefile.PL function
           INC  => "-I/usr/local/include/io_lib", # leave these as double quotes - necessary for Makefile.PL function
          );
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