configure

#! /bin/bash
# 
# This is a simple dropin for configure - so as to make life easier
# for newcomers to cmake.
#
# A number of switches gets translated use ./configure with:
#
#   --with-perl       : build biolib for Perl (default)
#   --with-ruby       : build biolib for Ruby
#   --with-python     : build biolib for Python
#
# In addition libraries can be specified

#   --with-staden     : see the BioLib docs
#   --with-emboss
#   --with-affyio
#   --with-rqtl
#   --with-libsequence
#   --with-example
#

if [ ! -d ./src ]; then
	echo "FATAL: run from the root of the Biolib tree"
	exit 1
fi

if [ -d .git ]; then
  if [ ! -e .git/SKIP_SUBMODULE_UPDATE ]; then
    echo "Checking for git submodules"
    git submodule update --init
		# Run these a few times to work around time outs
		git submodule update
		git submodule update
		git submodule update
	fi 
fi

language=$1
if [ -z $language ]; then
  language='--with-perl'
fi

case $language in
  '--help')
	echo "See the ./INSTALL document for configuration options"
	exit 1
	;;
  '--with-perl')
	plang="-DBUILD_PERL:BOOLEAN=TRUE"
	shift
	;;
  '--with-ruby')
	plang="-DBUILD_RUBY:BOOLEAN=TRUE"
	shift
	;;
  '--with-python')
	plang="-DBUILD_PYTHON:BOOLEAN=TRUE"
	shift
	;;
  *)
  echo "BioLib defaulting to Perl build"
	plang="-DBUILD_PERL:BOOLEAN=TRUE"
	library=$language
esac

if [ -z $library ]; then
  library=$1
	shift
fi

case $library in
  '--with-emboss')
	plib="-DEMBOSS_LIB:BOOLEAN=TRUE"
	shift
	;;
  '--with-staden')
	plib="-DSTADEN_LIB:BOOLEAN=TRUE"
	shift
	;;
  '--with-affyio')
	plib="-DAFFYIO_LIB:BOOLEAN=TRUE"
	shift
	;;
  '--with-libsequence')
	plib="-DLIBSEQUENCE_LIB:BOOLEAN=TRUE"
	shift
	;;
  '--with-rqtl')
	plib="-DRQTL_LIB:BOOLEAN=TRUE"
	shift
	;;
  '--with-example')
	plib="-DEXAMPLE_LIB:BOOLEAN=TRUE"
	shift
	;;
  *)
  echo "BioLib building all libraries"
	plib=""
esac

echo $language: $plang
echo $library: $plib

sh scripts/cleanup.sh

echo cmake $plang $plib $* . 
cmake $plang $plib $* .