#!/bin/bash

#++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#+   
#+     Mumps Bioinformatics Software Library
#+     Copyright (C) 2005, 2006 by Kevin C. O'Kane  
#+
#+     Kevin C. O'Kane
#+     anamfianna@earthlink.net
#+     okane@cs.uni.edu
#+
#+
#+ This program is free software; you can redistribute it and/or modify
#+ it under the terms of the GNU General Public License as published by
#+ the Free Software Foundation; either version 2 of the License, or
#+ (at your option) any later version.
#+ 
#+ This program is distributed in the hope that it will be useful,
#+ but WITHOUT ANY WARRANTY; without even the implied warranty of
#+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#+ GNU General Public License for more details.
#+ 
#+ You should have received a copy of the GNU General Public License
#+ along with this program; if not, write to the Free Software
#+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#+
#++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

# set the following parameters:

touch *.c *.cpp *.mps

autoconf

if [ $? != 0 ] ; then
	echo "errors in config.ac - terminating"
      exit
	fi

user="okane"
group="www"
amino_size=-1
nucl_size=-1
max_seq_length=25000
p_range=25000
p_min=100
high_limit=120
tmp_dir="/tmp"

# PRIMATES database setup
#db_files="gbpri"
#scale_factor=5
#nucl_size=11
#nbr_rand_smpls=25
#cp test.primates DATABASE/test
#cp pval.dat.invertebrates DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#database="/r0/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=65
#high_limit=100
#max_seq_length=25000
#p_range=25000

# RODENTS databse setup
#db_files="gbrod"
#scale_factor=5
#nucl_size=11
#nbr_rand_smpls=50
#cp test.rodents DATABASE/test
#cp pval.dat.rodents DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#max_seq_length=25000
#p_range=25000
#database="/c1/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=65

# VERTEBRATES database setup
#db_files="gbvrt"
#scale_factor=5
#nucl_size=11
#nbr_rand_smpls=25
#cp test.vertebrates DATABASE/test
#cp pval.dat.vertebrates DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#database="/c1/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=65
#high_limit=100
#max_seq_length=25000
#p_range=25000

# BACTERIA database setup
#db_files="gbbct"
#scale_factor=8
#nucl_size=11
#nbr_rand_smpls=25
#cp test.bacteria DATABASE/test
#cp pval.dat.bacteria DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#database="/c1/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=65
#high_limit=100
#max_seq_length=25000
#p_range=25000

# PLANT databse setup
#db_files="gbpln"
#scale_factor=5
#nucl_size=11
#nbr_rand_smpls=25
#cp test.plants DATABASE/test
#cp pval.dat.plants DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#database="/c1/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=65
#max_seq_length=25000
#p_range=25000

# INVERTEBRATES databse setup
#db_files="gbinv"
#scale_factor=1
#nucl_size=11
#nbr_rand_smpls=25
#cp test.invertebrates DATABASE/test
#cp pval.dat.invertebrates DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#database="/r0/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=65
#high_limit=100
#max_seq_length=25000
#p_range=25000

# PHAGE databse setup
#db_files="gbphg"
#scale_factor=1
#nucl_size=11
#nbr_rand_smpls=25
#cp test.phage DATABASE/test
#cp pval.dat.phage DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#database="/r0/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=65
#max_seq_length=25000
#p_range=25000

# VIRAL databse setup
#db_files="gbvrl"
#scale_factor=1
#nucl_size=11
#nbr_rand_smpls=25
#cp test.viral DATABASE/test
#cp pval.dat.phage DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#database="/r0/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=65
#max_seq_length=25000
#p_range=25000
#high_limit=120

# EST database setup
#db_files="gbest"
#scale_factor=5
#nucl_size=11
#nbr_rand_smpls=25
#cp test.est DATABASE/test
#cp pval.dat.est DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=1
#database="/c1/genbank"
#random="randomN"
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0
#low_limit=95
#high_limit=115
#max_seq_length=7500
#p_range=7500

# NT database setup
#db_files="nt"
#scale_factor=8
#nucl_size=11
#nbr_rand_smpls=25
#p_range=20000
#cp test.nt DATABASE/test
#cp pval.dat.nt DATABASE/pval.dat
#nucleotides="#define NUCLEOTIDES"
#extract_files=0
#database="/r0/blast/db/FASTA/nt"
#max_seq_length=20000
#random="randomN"
#low_limit=65
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0

# NR database setup
#db_files="nr"
#scale_factor=7
#nbr_rand_smpls=25
#cp pval.dat.nr DATABASE/pval.dat
#p_range=12000
#p_min=50
#max_seq_length=12000
#cp test.nr DATABASE/test
#database="/r0/blast/db/FASTA/nr"
#amino_size=3
#extract_files=0
#random="randomA"
#low_limit=30
#high_limit=65
# stat_cal - build new pval.dat data base if 1, don't if 0
#stat_calc=0

shred_home="http://sidhe.cs.uni.edu/cgi-bin/idf2"

#set the memory limit to a value less than your physical memory.

memlimit=1800000001

export database shred_home tmp_dir user group memlimit max_seq_length\
       nr_database nt_database nucleotides low_limit db_files scale_factor\
       nbr_rand_smpls extract_files amino_size random p_range high_limit stat_calc\
       nucl_size p_min

if [ $nucl_size = -1 ] && [ $amino_size = -1 ] ; then
      echo "No data base section was specified (uncommented)"
      echo "halting - configuration aborted"
      exit
      fi

./configure

if [ $? = 0 ] ; then
	echo "begin make"
	make idf
      cp blank.cgi DATABASE/statistics
      cp lm.cgi DATABASE/statistics
	chown $user *
	chgrp $group *
      chmod u+x stat.script
      chmod u+x DATABASE/statistics/setup.script
      chmod u+x DATABASE/clusterbuild.script
      chmod a+x DATABASE/index.cgi
      chmod a+x DATABASE/weights.cgi
else

      chown $user *
      chgrp $group *
	echo "make supressed due to errors from configure"
	fi