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* QUICK INSTRUCTIONS:
The configure script is a convenience wrapper. For a Perl build of biolib:
./configure
make
make test
make install
For a Ruby build:
./configure --with-ruby
make
make test
make install
For a Perl build:
./configure --with-perl
make
make test
make install
** Using CMake directly
The following makes the default libraries:
cmake .
make
make test
** Using Rake (with Ruby)
To install BioLib with Ruby support one can simply execute rake:
rake build
rake test
rake install
For installations specific to Perl, Python etc. see below.
* INSTALL biolib
Install or build the following tools on your system
gcc > 3.3.x (usually default on Linux)
cmake >= 2.6 (2008 distributions - needed for SWIG support)
swig >= 1.3.36 (2009 distributions)
python >= 2.4 (if you want Python support)
ruby >= 1.8.6 (if you want Ruby support)
perl >= 5.8.8 (if you want Perl support)
So for Debian you can do:
apt-get install g++ cmake swig r-base zlib1g-dev python ruby perl
see also ./doc/DEPENDENCIES.txt for more information on runtime libraries.
cmake 2.6 is available in Debian testing and etch-backports.
To build all Bio* biolib modules use:
./install.sh
which executes, essentially:
cmake .
make
make test
su -c make install
Now see if you can run the following:
ruby src/mappings/swig/ruby/test/test_example.rb
or,
ruby -I ./src/mappings/swig/ruby/example/ src/mappings/swig/ruby/test/test_example.rb
To change the default installation path use, for example:
cmake -DCMAKE_INSTALL_PREFIX=/opt/biolib .
make
make install
which puts the shared libraries in /opt/biolib/lib.
To have your programs find the shared libraries you may have to add '/usr/lib'
to ld.so.conf or add it the LD_LIBRARY_PATH.
The language specific libraries get copied into the language directories,
as modules.
** RUBY
To build BioLib RUBY libraries:
cmake -DBUILD_RUBY:BOOLEAN=TRUE .
make
ctest
su -c make install
** PYTHON
To build BioLib PYTHON libraries:
cmake -DBUILD_PYTHON:BOOLEAN=TRUE .
make
ctest
** PERL
To build BioLib PERL libraries:
cmake -DBUILD_PERL:BOOLEAN=TRUE .
make
ctest
** Build specific libraries only
Some libraries may have dependencies that are not relevant to your needs. For
example you may want to install the Staden for Perl only you can pass parameters:
sh scripts/cleanup.sh
cmake -DSTADEN_LIB:BOOLEAN=TRUE -DBUILD_PERL:BOOLEAN=TRUE .
make
su -c make install
** APIDOC
To build the API documentation (low-level 'C')
cmake -DBUILD_DOCS:BOOLEAN=TRUE .
make apidoc
** TROUBLE SHOOTING
When switching between build parameters make sure to remove the CMakeCache.txt
file in all directories. This can be achieved with sh ./scripts/cleanup.sh.
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