diff --git a/README b/README index 7d8a3de..427b3f6 100644 --- a/README +++ b/README @@ -1,15 +1,30 @@ - This is the directory for the Bioperl C compiled Extensions. -The main author for this is Ewan Birney +This is the directory for the Bioperl C compiled Extensions. - To install... +These currently include: - cd into Bio/Ext/Align - go perl Makefile.PL - make - make test (should print out alignment on STDERR) - make install (probably need root permissions). + Bio::Ext::Align (Ewan Birney ) + Bio::SeqIO::staden::read (Aaron Mackey ) +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 @@ -19,6 +34,27 @@ modules which do this are Bio::SearchDist - deals with EVD fitting of extreme value distributions For more information on how to use these modules, read their own documentation -(go perldoc Bio::Tools::pSW ...) +(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: + + ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/ + +The 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.