#!/usr/bin/perl use strict; #use Env; BEGIN{ @INC = ( '/bmlfast/bml_casp15/tools/casp14/DeepRank_db_tools/tools/SCRATCH-1D_1.1/perl_lib/', @INC ); } use Env; ########################################################################################## # # # Project : SCRATCH-1D # # Release : 1.1 # # # # File : install.pl # # Description : SCRATCH-1D installation script # # # # Author(s) : Christophe Magnan (cmagnan@ics.uci.edu) # # Copyright : Institute for Genomics and Bioinformatics # # University of California, Irvine # # # # Modified : 2015/07/02 # # # ########################################################################################## # Releases included in this package my $blast_release="blast-2.2.26"; my $brnn1d_release="1D-BRNN_3.3"; my $profilpro_release="PROFILpro_1.1"; my $homolpro_release="HOMOLpro_1.1"; my $sspro_release="SSpro_5.2"; my $sspro8_release="SSpro8_5.2"; my $accpro_release="ACCpro_5.2"; my $accpro20_release="ACCpro20_5.2"; # Retrieving installation path my $install_dir=`pwd`; chomp($install_dir); my $locerr="\nThis script must run from its own directory.\n"; if((! -d "$install_dir/bin")||(! -d "$install_dir/doc")){ print "$locerr\n"; exit 1; } if((! -d "$install_dir/env")||(! -d "$install_dir/lib")){ print "$locerr\n"; exit 1; } if((! -d "$install_dir/pkg")||(! -d "$install_dir/tmp")){ print "$locerr\n"; exit 1; } if(! -f "$install_dir/lib/check_project_profile.pl"){ print "$locerr\n"; exit 1; } if(! -f "$install_dir/lib/SCRATCH-1D_predictions.pl"){ print "$locerr\n"; exit 1; } if(! -f "$install_dir/lib/SCRATCH-1D_predictions.sh"){ print "$locerr\n"; exit 1; } if(! -f "$install_dir/lib/install_template1.sh"){ print "$locerr\n"; exit 1; } if(! -f "$install_dir/lib/install_template2.sh"){ print "$locerr\n"; exit 1; } if(! -f "$install_dir/lib/install_template3.sh"){ print "$locerr\n"; exit 1; } if(! -d "$install_dir/pkg/$blast_release"){ print "$locerr\n"; exit 1; } if(! -d "$install_dir/pkg/$brnn1d_release"){ print "$locerr\n"; exit 1; } if(! -d "$install_dir/pkg/$profilpro_release"){ print "$locerr\n"; exit 1; } if(! -d "$install_dir/pkg/$homolpro_release"){ print "$locerr\n"; exit 1; } if(! -d "$install_dir/pkg/$sspro_release"){ print "$locerr\n"; exit 1; } if(! -d "$install_dir/pkg/$sspro8_release"){ print "$locerr\n"; exit 1; } if(! -d "$install_dir/pkg/$accpro_release"){ print "$locerr\n"; exit 1; } if(! -d "$install_dir/pkg/$accpro20_release"){ print "$locerr\n"; exit 1; } print "\nInstalling SCRATCH-1D release 1.1...\nPath: $install_dir\n"; # Checking Blast Installation my @d=split("-",$blast_release); print "Checking blast (release $d[1]) installation...\n"; my $blast_install_dir="$install_dir/pkg/$blast_release"; if(! -f "$blast_install_dir/bin/blastall"){ print "blastall binary not found\n"; exit 1; } if(! -f "$blast_install_dir/bin/blastpgp"){ print "blastpgp binary not found\n"; exit 1; } # Installing 1D-BRNN Software @d=split("_",$brnn1d_release); print "Installing 1D-BRNN (release $d[1])...\n"; my $brnn1d_install_dir="$install_dir/pkg/$brnn1d_release"; if(! -f "$brnn1d_install_dir/src/makefile"){ print "1D-BRNN makefile not found\n"; exit 1; } `cd $brnn1d_install_dir/src; #chmod 777 *; make; make clean; #chmod 777 ../bin/*`; if(! -f "$brnn1d_install_dir/bin/predict_multi"){ print "1D-BRNN installation failed\n"; print "Please install a recent gcc compiler.\n"; exit 1; } # Installing PROFILpro Software @d=split("_",$profilpro_release); print "Installing PROFILpro (release $d[1])...\n"; my $profilpro_install_dir="$install_dir/pkg/$profilpro_release"; if(! -f "$profilpro_install_dir/install.pl"){ print "PROFILpro installer not found\n"; exit 1; } `cd $profilpro_install_dir; ./install.pl $install_dir/pkg $blast_install_dir`; if(! -f "$profilpro_install_dir/bin/generate_profiles.sh"){ print "PROFILpro installation failed\n"; exit 1; } if(! -f "$profilpro_install_dir/env/PROFILpro.sh"){ print "PROFILpro installation failed\n"; exit 1; } # Installing HOMOLpro Software @d=split("_",$homolpro_release); print "Installing HOMOLpro (release $d[1])...\n"; my $homolpro_install_dir="$install_dir/pkg/$homolpro_release"; if(! -f "$homolpro_install_dir/install.pl"){ print "HOMOLpro installer not found\n"; exit 1; } `cd $homolpro_install_dir; ./install.pl $install_dir/pkg $blast_install_dir`; if(! -f "$homolpro_install_dir/bin/add_homology_predictions.sh"){ print "HOMOLpro installation failed\n"; exit 1; } if(! -f "$homolpro_install_dir/env/HOMOLpro.sh"){ print "HOMOLpro installation failed\n"; exit 1; } # Installing SSpro Software my $dependencies="$profilpro_install_dir $homolpro_install_dir $brnn1d_install_dir"; @d=split("_",$sspro_release); print "Installing SSpro (release $d[1])...\n"; my $sspro_install_dir="$install_dir/pkg/$sspro_release"; if(! -f "$sspro_install_dir/install.pl"){ print "SSpro installer not found\n"; exit 1; } `cd $sspro_install_dir; ./install.pl $dependencies`; my $sspro_error="SSpro installation failed"; if(! -f "$sspro_install_dir/env/SSpro.sh"){ print "$sspro_error\n"; exit 1; } if(! -f "$sspro_install_dir/bin/sequence_to_ss.sh"){ print "$sspro_error\n"; exit 1; } if(! -f "$sspro_install_dir/bin/sequence_to_ss_ab.sh"){ print "$sspro_error\n"; exit 1; } if(! -f "$sspro_install_dir/bin/profiles_to_ss.sh"){ print "$sspro_error\n"; exit 1; } if(! -f "$sspro_install_dir/bin/profiles_to_ss_ab.sh"){ print "$sspro_error\n"; exit 1; } if(! -f "$sspro_install_dir/data/models.txt"){ print "$sspro_error\n"; exit 1; } # Installing SSpro8 Software @d=split("_",$sspro8_release); print "Installing SSpro8 (release $d[1])...\n"; my $sspro8_install_dir="$install_dir/pkg/$sspro8_release"; if(! -f "$sspro8_install_dir/install.pl"){ print "SSpro8 installer not found\n"; exit 1; } `cd $sspro8_install_dir; ./install.pl $dependencies`; my $sspro8_error="SSpro8 installation failed"; if(! -f "$sspro8_install_dir/env/SSpro8.sh"){ print "$sspro8_error\n"; exit 1; } if(! -f "$sspro8_install_dir/bin/sequence_to_ss8.sh"){ print "$sspro8_error\n"; exit 1; } if(! -f "$sspro8_install_dir/bin/sequence_to_ss8_ab.sh"){ print "$sspro8_error\n"; exit 1; } if(! -f "$sspro8_install_dir/bin/profiles_to_ss8.sh"){ print "$sspro8_error\n"; exit 1; } if(! -f "$sspro8_install_dir/bin/profiles_to_ss8_ab.sh"){ print "$sspro8_error\n"; exit 1; } if(! -f "$sspro8_install_dir/data/models.txt"){ print "$sspro8_error\n"; exit 1; } # Installing ACCpro Software @d=split("_",$accpro_release); print "Installing ACCpro (release $d[1])...\n"; my $accpro_install_dir="$install_dir/pkg/$accpro_release"; if(! -f "$accpro_install_dir/install.pl"){ print "ACCpro installer not found\n"; exit 1; } `cd $accpro_install_dir; ./install.pl $dependencies`; my $accpro_error="ACCpro installation failed"; if(! -f "$accpro_install_dir/env/ACCpro.sh"){ print "$accpro_error\n"; exit 1; } if(! -f "$accpro_install_dir/bin/sequence_to_acc.sh"){ print "$accpro_error\n"; exit 1; } if(! -f "$accpro_install_dir/bin/sequence_to_acc_ab.sh"){ print "$accpro_error\n"; exit 1; } if(! -f "$accpro_install_dir/bin/profiles_to_acc.sh"){ print "$accpro_error\n"; exit 1; } if(! -f "$accpro_install_dir/bin/profiles_to_acc_ab.sh"){ print "$accpro_error\n"; exit 1; } if(! -f "$accpro_install_dir/data/models.txt"){ print "$accpro_error\n"; exit 1; } # Installing ACCpro20 Software @d=split("_",$accpro20_release); print "Installing ACCpro20 (release $d[1])...\n"; my $accpro20_install_dir="$install_dir/pkg/$accpro20_release"; if(! -f "$accpro20_install_dir/install.pl"){ print "ACCpro20 installer not found\n"; exit 1; } `cd $accpro20_install_dir; ./install.pl $dependencies`; my $accpro20_error="ACCpro20 installation failed"; if(! -f "$accpro20_install_dir/env/ACCpro20.sh"){ print "$accpro20_error\n"; exit 1; } if(! -f "$accpro20_install_dir/bin/sequence_to_acc20.sh"){ print "$accpro20_error\n"; exit 1; } if(! -f "$accpro20_install_dir/bin/sequence_to_acc20_ab.sh"){ print "$accpro20_error\n"; exit 1; } if(! -f "$accpro20_install_dir/bin/profiles_to_acc20.sh"){ print "$accpro20_error\n"; exit 1; } if(! -f "$accpro20_install_dir/bin/profiles_to_acc20_ab.sh"){ print "$accpro20_error\n"; exit 1; } if(! -f "$accpro20_install_dir/data/models.txt"){ print "$accpro20_error\n"; exit 1; } # Preparing SCRATCH-1D bash profile print "Installing SCRATCH-1D bash profile...\n"; open(IN,"$install_dir/lib/install_template1.sh"); open(OUT,">$install_dir/env/SCRATCH-1D.sh"); while(my $l=){ chomp($l); if($l eq ""){ print OUT "export SCRATCH1D_ROOT_DIR=\"$install_dir\"\n"; } elsif($l eq ""){ print OUT "export PROFILpro_INSTALL_DIR=\"$profilpro_install_dir\"\n"; } elsif($l eq ""){ print OUT "export SSpro_INSTALL_DIR=\"$sspro_install_dir\"\n"; } elsif($l eq ""){ print OUT "export SSpro8_INSTALL_DIR=\"$sspro8_install_dir\"\n"; } elsif($l eq ""){ print OUT "export ACCpro_INSTALL_DIR=\"$accpro_install_dir\"\n"; } elsif($l eq ""){ print OUT "export ACCpro20_INSTALL_DIR=\"$accpro20_install_dir\"\n"; } elsif($l eq ""){ print OUT "export HOMOLpro_INSTALL_DIR=\"$homolpro_install_dir\"\n"; } else{ print OUT "$l\n"; } } close(IN); close(OUT); #`chmod 777 $install_dir/env/SCRATCH-1D.sh`; # Preparing SCRATCH-1D launchers print "Installing SCRATCH-1D bin scripts...\n"; open(IN,"$install_dir/lib/install_template2.sh"); open(OUT,">$install_dir/bin/run_SCRATCH-1D_predictors.sh"); while(my $l=){ chomp($l); if($l eq ""){ print OUT "install_dir=\"$install_dir\"\n"; } else{ print OUT "$l\n"; } } close(IN); close(OUT); #`chmod 777 $install_dir/bin/run_SCRATCH-1D_predictors.sh`; open(OUT,">$install_dir/bin/get_abinitio_predictions.sh"); open(IN,"$install_dir/lib/install_template3.sh"); while(my $l=){ chomp($l); if($l eq ""){ print OUT "install_dir=\"$install_dir\"\n"; } else{ print OUT "$l\n"; } } close(IN); close(OUT); #`chmod 777 $install_dir/bin/get_abinitio_predictions.sh`; # Print message to test installation print "\nSCRATCH-1D successfully installed...\n\nTo test the installation:\n\n"; print "Change directory to the 'doc' sub-folder\n\n cd doc\n\n"; print "Run SCRATCH-1D on the provided test datasets:\n\n"; print " ../bin/run_SCRATCH-1D_predictors.sh test.fasta test.out 4\n\n"; print "The output files 'test.out.*' should be identical to 'test.hom.*'\n\n";