rp_config

#!/usr/bin/env perl
use strict;
use File::Basename;
use Cwd;
use Data::Dumper;

### Script to configure settings for ricopili pipeline
### Jackie Goldstein, Jan 2014 & stephan ripke 2016


my $version = "2.0.0";
my $progname = $0;

$progname =~ s!^.*/!!;

my $rp_custom_installation_file = "rp_config.custom.txt";


my $custom_txt = "
-----------------------------------------------
------------ CUSTOM INSTALLATION --------------
-----------------------------------------------

- please download and extract the following tarball to a different, empty directory (please remember the full path of this directory since you will need it during this process), with this tarball you will get most necessary binaries and resource files
- follow the instructions in its README (README.binaries).

e.g.:

mkdir rp_dependenscies
cd rp_dependenscies
wget https://personal.broadinstitute.org/sripke/share_links/doMoVLWDcLcasit7xlcmwtt7cxDMjq_Ricopili_Dependencies.0918/Ricopili_Dependencies.0918.tar.gz .



after that start rp_config choosing cluster environment -custom- (choice 10).
if customfile ($rp_custom_installation_file) is not present this rp_config will write out a template to be filled out by you

";

##### help message
my $usage = "
Usage : $progname [options] --help



 --help                print this text and exits
 --customfile STRING   different customfile than default $rp_custom_installation_file

 --rphome STRING       different homedirectory for ricopili.conf (by default it is environement HOME)
 --depdir STRING       replace expression DEPDIR with STRING in the customfile (e.g. dependency_directory tends to get used multiple times)


 this script is trying to make the configuration of the ricopili pipeline as convenient as possible.
 you will be able to choose from a variety of preset computer clusters.

 since october 2018 this configuration is customizable:
    - this is the preferred method since it only needs the right configuration file and not any changes of the sourcecode
 


please follow this document: https://docs.google.com/document/d/14aa-oeT5hF541I8hHsDAL_42oyvlHRC5FWR7gir4xco/edit?usp=sharing



    ";


my $old_txt = "

###############################
### I think this if found in the README anyway and can go from these instructions
#######################################



most recent addition: 

-----------------------------------------------------------
in location of bcrloc needs to be this file
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz

found on broad here:
/psych/genetics_data/ripke/rp_bins/bcftools/bcftools-1.3.1/resources/human_g1k_v37.fasta
    
--------------------------------------------------------------

in location of bcloc needs to be this binray:
bcftools

found on broad here:
/psych/genetics_data/ripke/rp_bins/bcftools/new_0816/bcftools-1.3.1_bin/bin/bcftools


----------------------------------------------------------------------

### Jackie Goldstein, Jan 2014 & stephan ripke 2016
########################################################

    ";


my $custom_file_template = '
### for details please refer to https://docs.google.com/document/d/14aa-oeT5hF541I8hHsDAL_42oyvlHRC5FWR7gir4xco/edit?usp=sharing
###          and https://docs.google.com/spreadsheets/d/1LhNYIXhFi7yXBC17UkjI1KMzHhKYz0j2hwnJECBGZk4/edit?usp=sharing
variable_name                  variable_value
----------------------------------------------
rp_dependencies_dir                              
R_packages_dir                                   
starting_R                                       
path_to_Perlmodules                              
path_to_scratchdir                               
starting_ldsc
ldsc_reference                                    
rp_user_initials                                 
rp_user_email                                    
rp_logfiles                                      
----------------------------------------
----------------------------------------
---- jobarray and queueing parameters: 
----------------------------------------
----------------------------------------
serial 0
batch_jobcommand                                 
batch_memory_request                             
batch_walltime                                   
batch_array                                      
batch_max_parallel_jobs_per_one_array            
batch_jobfile                                    
batch_name                                       
batch_stdout                                     
batch_stderr                                     
batch_job_dependency                             
batch_array_task_id                              
batch_other_job_flags        NONE                           
batch_job_output_jid                             
batch_ncores_per_node        NA
batch_mem_per_node           NA
';




my $rphome = $ENV{HOME};


use Getopt::Long;
GetOptions( 
    
    "help"=> \my $help,
    "customfile=s"=> \$rp_custom_installation_file,
    "rphome=s"=> \$rphome,
    "depdir=s"=> \my $depdir,
    
    );


if ($help) {
    print $usage ;
    exit;
}



###################################################
###  waiting for user to continue
###################################################
sub cont(){
    print "continue (y/n)?\n";
    my $answer = lc <>;
    chomp $answer;
    unless ($answer eq "y") {
	print "exiting.....\n";
	exit;
    }
}



my $welcome_message = '
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
-------------------------   RP_CONFIG    ------------------------------------
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
 Script to ease Downloading, Configuration, Installation of Ricopili
-----------------------------------------------------------------------------
        please use flag --help if you are not familiar with its usage
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
';

print "$welcome_message\n";
#&cont();



my %bin_names;
my %bin_locs;




#####################
# plink: just download
#####################
$bin_names{"plink"} = "plink";
$bin_locs{"plink"} = "https://www.cog-genomics.org/static/bin/plink170330/plink_linux_x86_64.zip";

########################
# shapeit: download and detar and copy binary from bin subdir to root
###########################
$bin_names{"shapeit"} = "shapeit.v2.r837.linux.x86_64";
$bin_locs{"shapeit"} = "https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r837.GLIBCv2.12.Linux.static.tgz";

########################
# impute: download, detar and point to subdir
###########################
$bin_names{"impute"} = "impute_v2.3.2_x86_64_static/impute2";
$bin_locs{"impute2"} = "https://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_x86_64_static.tgz";


################################
# eigenstrat
################################
$bin_names{"eigenstrat"} = "bin/smartpca";
$bin_locs{"eigenstrat"} = "https://data.broadinstitute.org/alkesgroup/EIGENSOFT/EIG-6.1.4.tar.gz";


############
## LDSCORE????
######################


############
## liftOver
######################
$bin_names{"liftover"} = "liftOver";
$bin_locs{"liftover"} = "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver";





    #############################################################
    ### for better installation
    #########################################################
    
#  http://hgdownload.soe.ucsc.edu/goldenPath/hg17/liftOver/hg17ToHg19.over.chain.gz
#  http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz
#  http://hgdownload.soe.ucsc.edu/goldenPath/hg16/liftOver/hg16ToHg19.over.chain.gz
#  http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
    
#  http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg18.over.chain.gz

#    grep in rp_bin for other liloc files:
#    grep liloc *




    
#print "fasta file to bcftools directory:\n";
#print "/psych/genetics_data/ripke/rp_bins/bcftools/bcftools-1.3.1/resources/human_g1k_v37.fasta:\n";
#print "## ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz\n";
#exit;




my $cdir = cwd();
my $home = $ENV{HOME};
my $conf_file = $rphome."/ricopili.conf";
my $command_line = "$progname @ARGV";

#############################
# Ask user what cluster they're using
#############################
#my %clusters = ("broad",0,"mssm",0,"genomedk",0,"lisa",0,"other",0);
#my %clusters = ("broad",0,"mssm",0,"genomedk",0,"lisa",0,"computerome",0,"other",0);
#my %clusters = ("broad",0,"mssm",0,"genomedk",0,"lisa",0,"computerome",0,"co_ipsych",0,"uppmax",0,"other",0);
my %clusters = ("broad_do_not_use",0,"mssm_do_not_use",0,"genomedk_do_not_use",0,"lisa_do_not_use",0,"computerome_do_not_use",0,"co_ipsych_do_not_use",0,"uppmax_do_not_use",0,"unc_slurm_do_not_use",0,"bih_qsub_do_not_use",0,"custom",0);
my @cluster_names = ("broad_do_not_use","mssm_do_not_use","genomedk_do_not_use","lisa_do_not_use","computerome_do_not_use","co_ipsych_do_not_use","uppmax_do_not_use","unc_slurm_do_not_use","bih_qsub_do_not_use","custom");


my $cluster = "custom";
$clusters{custom} = 1;

if (0) {
print "Please enter your cluster environment from the following options:\n";
print "!!!! since the 1018 versions only custom (10) !!!!!\n";
my $i = 1;
foreach (@cluster_names){
    unless ($_ =~ /do_not_use/) {
	print "\t($i) $_\n";
    }
    $i += 1;
}
print "\n";

while (1) {    
    $cluster = lc <>;
    chomp $cluster;
    if (exists $clusters{$cluster}){$clusters{$cluster} = 1;last;}
    else {
	$cluster =~ s/(\)|\()//g;
	if ($cluster >= 1 && $cluster <= $i){$cluster -= 1; $cluster = $cluster_names[$cluster];$clusters{$cluster} = 1;last;}
	else {
	    print "Did not recognize option. Please enter a cluster name from the options below:\n";
	    my $i = 1;
	    foreach (@cluster_names){
		print "\t($i) $_\n";
		$i += 1;
	    }
	    print "\n";
	    my $cluster = "other";
	}
    }
}
}

print "\nUsing the following cluster: $cluster\nin combination with $rp_custom_installation_file\n\n";
sleep (2);
#exit;

#################################################################################
###### CUSTOM configuration file
################################################################################


my %conf;
$conf{"batch_ncores_per_node"} = "NA";
$conf{"batch_mem_per_node"} = "NA";
    

if ($clusters{custom}){
    if (-e $rp_custom_installation_file) {
	die $!."($rp_custom_installation_file)" unless open FILE, "< $rp_custom_installation_file";
	while (my $line = <FILE>){
	    unless ($line =~ /^\-\-\-/ || $line =~ /^\*\*/) {
		$line =~ s/###.*//;
		my @cells = split /\s+/, $line;

		if ($depdir) {
		    $cells[1]=~ s/DEPDIR/$depdir/g;
		}

		
		unless ($cells[0] eq "" || $cells[0] eq "variable") {
		    $conf{$cells[0]} = $cells[1];
		    #	    my $line =~ s/^$cells[0]//;
		    print "<".$cells[0].">"." <".$cells[1].">\n";
		}
	    }
	}
	close FILE;
    }
    else {
	print "-----------------------------------------------------------------\n";
	print "-----------------------------------------------------------------\n";
	print "Custom - File ($rp_custom_installation_file) not found\n";
	
	die $!."($rp_custom_installation_file)" unless open FILE, "> $rp_custom_installation_file";
	#    print FILE "exbin_dir PLACEHOLDER ## directory in which all downloaded external binaries will be installed to\n";
	print FILE $custom_file_template;
	close FILE;

	print "-> an empty one was now created, please fill and restart rp_config afterwards\n\nExit now\n\n";
	exit;
	
    }


#    print "$custom_txt\n";
}



my $path_to_perlmodules = $conf{"path_to_Perlmodules"};

if ($path_to_perlmodules eq "") {
    if ($clusters{custom}){ 
	print "Error: <path_to_Perlmodule> is not set in $rp_custom_installation_file\n";
	exit;
    }
}





# If on an Uppmax cluster, determine which one, and which account to use.
# Uses code from the projinfo utility on Uppmax
my $uppmax_project;
my $uppmax_cluster;
my $username;
if ($clusters{uppmax}) {
    # get username
    $username = getlogin || getpwuid($<);

    # get cluster name
    open CONFIG, "scontrol show conf 2>&1 |"
      or die "Error: Cannot find SLURM configuration.\n";
    while (<CONFIG>) {
        chomp;
        my $line = lc $_;

        if ($line =~ /^clustername\s+=\s+(\S+)\s*$/) {
            $uppmax_cluster = $1;
            last
        }
    }
    close CONFIG;

    # get user's current projects
    my $grantfile = "/sw/share/slurm/$uppmax_cluster/grantfile";
    my @uppmax_projects;

    open GRANTFILE, "< $grantfile"
      or die "Error: Cannot read file $grantfile.\n";
    while (<GRANTFILE>) {
        chomp;
        my $line = $_;
        next if /^\s*$/;        # Empty line
        next if /^\s*#/;        # Comment
        if (/^([^,]+),[^,]+,([^,]+),[^#]+#(.*)$/) {
            my $projectname = $1;
            my $grant = $2;
            my $members = $3;
            if ($members =~
                /^$username$|^$username\s|\s$username\s|\s$username$/)
            {
                push @uppmax_projects, $projectname;
            }
        }
        elsif (/^([^:]+):(\d+):.*:([^:]*)$/) {
            my $projectname = $1;
            my $grant = $2;
            my $members = $3;
            if ($members =~ /^$username$|^$username,|,$username,|,$username$/) {
                push @uppmax_projects, $projectname;
            }
        }
        else { # Error in file
            die "Error: Bad line in file $grantfile:\n\t$line\n";
        }
    }
    close GRANTFILE;

    # choose project (account) to use with ricopili
    print "Please choose the Uppmax project you want to use with ricopili:\n";
    my $i = 1;
    foreach (@uppmax_projects){
        print "\t($i) $_\n";
        $i += 1;
    }
    print "\n";
    while (1) {
        my $project = lc <>;
        chomp $project;
        if ( grep(/^$project$/, @uppmax_projects) ){ $uppmax_project = $project; last;}
        else {
            $project =~ s/(\)|\()//g;
            if ($project >= 1 && $project <= $i){
                $project -= 1;
                $uppmax_project = $uppmax_projects[$project];
                last;
            }
            else {
                print "Did not recognize option. Please enter a project identifier from the options below:\n";
                my $i = 1;
                foreach (@uppmax_projects){
                    print "\t($i) $_\n";
                    $i += 1;
                }
                print "\n";
            }
        }
    }
    print "\nUsing the following Uppmax project: $uppmax_project\n\n";
}

    
#############################
# Determine the shell
#############################
my $shell = '';
if (exists $ENV{SHELL}){$shell = basename($ENV{SHELL});}
if ($shell eq "bash-login-check"){$shell = "bash";}
if ($shell ne "bash" && $shell ne "tcsh") {
    print "Warning! Shell not recognized: $shell\n";
    print "Please send email to rp_dev\@broadinstitute.org\n";
}
print "Detected you are using the following shell: $shell\n\n";


#############################
# Determine the shell-bashrc
#############################

## just for info
my $bashrc = "";
if (-e "$home/.my.bashrc") {
    $bashrc = "$home/.my.bashrc";
    print " - bash detected - \n\n";
}
elsif (-e "$home/.bashrc") {
    $bashrc = "$home/.bashrc";
    print " - bash detected - \n\n";
}
elsif (-e "$home/.my.cshrc") {
    $bashrc = "$home/.my.cshrc";
    print " - csh detected - \n\n";
}
elsif (-e "$home/.cshrc") {
    $bashrc = "$home/.my.cshrc";
    print " - csh detected - \n\n";
}
else {
    print "Could not find any shell-starting files ($home/.bashrc or $home/.cshrc)\n";
    print "please consult your admins how to achieve the above tasks\n";
}





###################################################
###  system call with test if successful
###################################################
sub mysystem(){
    my ($systemstr)="@_";
    system($systemstr);
    my $status = ($? >> 8);
    die "$systemstr\n->system call failed: $status" if ($status != 0);
}


###################################################
###  Check if rp_bin already installed
###################################################
system("bin_check"); # dummy script that doesn't do anything
my $status_bin = ($? >> 8);
system("bin_check_pdfjam"); # dummy script that doesn't do anything
my $status_pdfjam = ($? >> 8);


if ($clusters{lisa} == 1) {
    unless (-e "$home/.bash_profile") {
	die $! unless open FILE, "> $home/.bash_profile";
	     print FILE 'if [ -f ~/.bashrc ]; then '."\n";
	     print FILE '    . ~/.bashrc'."\n";
	     print FILE 'fi'."\n";
	close FILE;
    }
    unless (-e "$home/.bashrc") {
	system "touch ~/.bashrc\n";
    }
}




    
if ($status_bin == 0  && $status_pdfjam == 0 &&  !(-e "install_true")) {
    print "\n----------------------------------------------------\n";                    
    print "\n\nWarning: Ricopili is already installed.\n";
    print "Do you wish to uninstall the Ricopili PATH settings first (recommended)? <y/n>\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {

            print "\n\n";
	    print "*********************************************************************\n";
	    print "*****  please read and follow instructions below, *******************\n";
	    print "*****              only then restart ./rp_config  *******************\n";
	    print "**********************************************************************\n";
	    print "\n\n";	    




	    
	    print "\nJust for your information, the following commands will remove the following paths from your your current session and also for future logins:\n\n";


            my @PATH = split(':',$ENV{PATH});
            foreach (@PATH) {
                if ($_ =~ "rp_bin" || $_ =~ "rp_perlpackages") {
                    print "\t$_\n";}
            }

            
            my @PATH = split ":", $ENV{PATH};
            my @NEW_PATH = ();
	    my $path_found = 0;
            foreach (@PATH) {
                unless ($_ =~ "rp_bin") {
                    push @NEW_PATH, $_;
                }
		else {
		    $path_found = 1;
		}
            }

	    if ($path_found == 1) {

		my $new_path = join ":", @NEW_PATH;

		my $i = 1;
		print "\n1) Run this command (copy/paste an return) to remove rp_bin from the search path in your current login session\n\n";
		
		# 1. Remove paths for this session
		if ($shell eq "bash") {
		    $i += 1;                
		    print "\texport PATH=$new_path\n\n";
		}
		elsif ($shell eq "tcsh") {
		    $i += 1;                                
		    print "\tsetenv PATH $new_path\n\n";
		}
		else {
		    print "   ---- shell seems to be different to bash or tcsh                                -------------\n";
		    print "   ---- please figure out how to change the current search path to the following   -------------\n";
		    $i += 1;
		    print "\t$new_path\n";
		}
	    }

	    
	    ###############################################################################
            # 2. Remove the path permanently from the search path

	    my $perma_found = 0;
	    my $found_txt = "";


	    if ($bashrc ne "") {


		my @tmp_lines = `grep rp_bin $bashrc`;
		$perma_found += @tmp_lines;
		foreach (@tmp_lines) {
		    $found_txt .= "\t\t\t$_";
		}
		@tmp_lines = `grep rp_perlpackages $bashrc`;
		$perma_found += @tmp_lines;
		foreach (@tmp_lines) {
		    $found_txt .= "\t\t\t$_";
		}


		if ($perma_found > 0){


		    
                    &mysystem("grep -v rp_bin $bashrc | grep -v rp_perlpackages > $bashrc.minus_rpbin.txt");
                    &mysystem("cp $bashrc $bashrc.copy");


#                    $i += 1;

		    print "\n2) Run this command to remove rp_bin permanantly from the search path.\n";
                    print "\n\tmv $bashrc.minus_rpbin.txt $bashrc\n\n";
		    print "\t\t## this will delete the following lines from your $bashrc file:\n\n";
                    print "$found_txt\n";
		    
		  		    

                    print "\n\t\t-> a backup of $bashrc is available here: $bashrc.copy\n";                    
                }
		else {


		}

            }
	    #            elsif ($clusters{genomedk} == 1 || $clusters{mssm} == 1 || $clusters{lisa} == 1 || $clusters{computerome} == 1 || $clusters{co_ipsych} == 1 || $clusters{uppmax} == 1) {


	    

#            else {
#                print "\n----------------------------------------------------\n";                                    
#                print "\n## Remove the directories listed above from the same place where you permanently added the directories to the search path.\n";
#                $i += 1;
#            }
	    
            print "\n\n";
	    print "*********************************************************************\n";
	    print "*********************************************************************\n";
	    print "*****  please read and follow instructions above, *******************\n";
	    print "*****              only then restart ./rp_config  *******************\n";
	    print "**********************************************************************\n";
	    print "\n\n";
            exit;
        }
        elsif ($answer eq "n") {&mysystem("touch install_true");last;}
        else {print "Please answer with y or n.\n";}
    }
};

###################################################
###  Add rp_bin to default search path
###################################################
system("bin_check"); # dummy script that doesn't do anything
my $status_bin = ($? >> 8);
system("bin_check_pdfjam"); # dummy script that doesn't do anything
my $status_pdfjam = ($? >> 8);




# exit;


unless ($status_bin == 0  && $status_pdfjam == 0) {    
    my $bash = "$cdir/my.bashrc_rp_path";    
    my $csh = "$cdir/my.cshrc_rp_path";    

    die $! unless open FILE, "> $bash";
    print FILE "\n\nPATH=$cdir:\$PATH\n";
    print FILE "PATH=$cdir/pdfjam:\$PATH\n";
    
    if ($clusters{lisa}){
        print FILE "\texport rp_perlpackages=/home/gwas/perl_modules\n";
    }
    if ($clusters{computerome}){
        print FILE "\texport rp_perlpackages=/home/people/sripke/rp_external_bins/perl_packages\n";
    }
    if ($clusters{co_ipsych}){
        print FILE "\texport rp_perlpackages=/data/user_tools/rp_external_bins/perl_packages\n";
    }    
    if ($clusters{broad}){
        print FILE "\texport rp_perlpackages=/home/unix/sripke/perl_modules\n";
    }
    if ($clusters{uppmax}){
        print FILE "\texport rp_perlpackages=/proj/$uppmax_project/ricopili/software/perl_modules\n";
    }
    if ($clusters{custom}){
        print FILE "\texport rp_perlpackages=$path_to_perlmodules\n";
	print FILE "\texport RPHOME=$rphome\n";
    }
    close FILE;

    if ($clusters{custom}){
	die $! unless open FILE, "> $csh";
	print FILE "\n\nset path=($cdir \$path)\n";
	print FILE "set path=($cdir/pdfjam \$path)\n";
	if ($clusters{broad}){
	    print FILE "setenv rp_perlpackages $path_to_perlmodules\n";
	    print FILE "setenv RPHOME $rphome\n";
	}
	close FILE;
    }


    print "\n\n";
    print "*********************************************************************\n";
    print "*** Setting the path (permanantly and for this sesion ***************\n";
    print "***     for the ricopili scripts and for pdfjam       ***************\n";
    print "*********************************************************************\n";
    print "\n";

    print "*********************************************************************\n";
    print "*****  please read and follow instructions below, *******************\n";
    print "*****              only then restart ./rp_config  *******************\n";
    print "**********************************************************************\n";
    print "\n\n";

    print "## Please run the following commands to permanently add rp_bin to the default search path: \n";
    print "##     (the last two add the necessary paths also to your current session) \n\n";


    if ($clusters{broad}){
        my $i = 1;
       
        if (-e "$home/.my.bashrc") {
            print "\tcat $bash >> ~/.my.bashrc\n";
            $i += 1;
        }
        if (-e "$home/.my.cshrc") {
            print "\tcat $csh >> ~/.my.cshrc\n";
            $i += 1;
        }

        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;
            print "\texport rp_perlpackages=/home/unix/sripke/perl_modules\n";
            $i += 1;
        }
        elsif ($shell eq "tcsh") {
            print "\tset path=($cdir \$path)\n";
            $i += 1;
            print "\tset path=($cdir/pdfjam \$path)\n";
            $i += 1;
            print "\tsetenv rp_perlpackages /home/unix/sripke/perl_modules\n";
            $i += 1;
        }

    }
    elsif ($clusters{genomedk}){
	my $i = 1;
	

        if (-e "$home/.bashrc") {
            print "\tcat $bash >> ~/.bashrc\n";
            $i += 1;
        }
        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;        
        }

    }
    elsif ($clusters{lisa}){
	my $i = 1;    

        if (-e "$home/.bashrc") {
            print "\tcat $bash >> ~/.bashrc\n";
            $i += 1;
        }
        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;        
        }
	print "\texport rp_perlpackages=/home/gwas/perl_modules\n";
    }
    elsif ($clusters{computerome}){
	my $i = 1;    

        if (-e "$home/.bashrc") {
            print "\tcat $bash >> ~/.bashrc\n";
            $i += 1;
        }
        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;        
        }
	print "\texport rp_perlpackages=/home/people/sripke/rp_external_bins/perl_packages\n";
    }
    
    elsif ($clusters{co_ipsych}){
	my $i = 1;    

        if (-e "$home/.bashrc") {
            print "\tcat $bash >> ~/.bashrc\n";
            $i += 1;
        }
        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;        
        }
	print "\texport rp_perlpackages=/data/user_tools/rp_external_bins/perl_packages\n";
    }

    elsif ($clusters{mssm}){
	my $i = 1;    

        if (-e "$home/.bashrc") {
            print "\tcat $bash >> ~/.bashrc\n";
            $i += 1;
        }
        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;        
        }
    }
    
    elsif ($clusters{bih_qsub}){
	my $i = 1;    

        if (-e "$home/.bashrc") {
            print "\tcat $bash >> ~/.bashrc\n";
            $i += 1;
        }
        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;        
        }
    }
    
    elsif ($clusters{unc_slurm}){
	my $i = 1;    

        if (-e "$home/.bashrc") {
            print "\tcat $bash >> ~/.bashrc\n";
            $i += 1;
        }
        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;        
        }
    }



    elsif ($clusters{custom}){
	my $i = 1;    
	if ($shell eq "bash") {
	    print "\tcat $bash >> $bashrc\n";
	    $i += 1;
	    print "\tPATH=$cdir:\$PATH\n";
	    $i += 1;
	    print "\tPATH=$cdir/pdfjam:\$PATH\n";
	    $i += 1;
	    print "\texport rp_perlpackages=$path_to_perlmodules\n";
	    print "\texport RPHOME=$rphome\n";
	    $i += 1;
	}

	if ($shell eq "tcsh") {
	    print "\tcat $csh >> $bashrc\n";
	    $i += 1;
            print "\tset path=($cdir \$path)\n";
            $i += 1;
            print "\tset path=($cdir/pdfjam \$path)\n";
            $i += 1;
            print "\tsetenv RPHOME $rphome\n";
            $i += 1;
	}
	
    }
    
    

    elsif ($clusters{uppmax}){
	my $i = 1;

        if (-e "$home/.bashrc") {
            print "\tcat $bash >> ~/.bashrc\n";
            $i += 1;
        }
        if ($shell eq "bash") {
            print "\tPATH=$cdir:\$PATH\n";
            $i += 1;
            print "\tPATH=$cdir/pdfjam:\$PATH\n";
            $i += 1;
        }
	print "\texport rp_perlpackages=/proj/$uppmax_project/ricopili/software/perl_modules\n";

    }

    else {
        print "You'll need to add the following paths to your default search path:\n";
        print "\t$cdir\n";
        print "\t$cdir/pdfjam\n\n";
        print "If you are using a bash shell, sample commands are located in this file: $bash\n";
        print "If you are using a tcsh shell, sample commands are located in this file: $csh\n";
        print "For example instructions, see http://www.cyberciti.biz/faq/unix-linux-adding-path/\n";
        print "If possible, add these paths permanently. Otherwise, you will need to do this everytime you start a new session.\n";
    }
    
    &mysystem("touch install_true");        
    print "\n\n";
    print "*********************************************************************\n";
    print "*****  please read and follow instructions above, *******************\n";
    print "*****              only then restart ./rp_config  *******************\n";
    print "**********************************************************************\n";
    print "\n\n";
    exit;

}

print "Required directories found in search path:\n";
print "\trp_bin/ -- success\n";
print "\trp_bin/pdfjam/ -- success\n\n";

system("latex small2e > /dev/null"); # dummy script that doesn't do anything
my $status_latex = ($? >> 8);
unless ($status_latex) {
    print "Detected latex is installed.\n\n";
    &mysystem("rm small2e.*");
}
else {
    print "---------------------------------------\n\n";
    print "Error -- latex is not installed!\n\n";

    if ($clusters{genomedk} == 1){
	print "Run the following commands to add latex to the default search path:\n";
	print "\techo \"source /com/extra/texlive/2014/load.sh\" >> ~/.bashrc\n";
	print "\tsource /com/extra/texlive/2014/load.sh\n\n";
    }
    else {
	print "Please install pdflatex by downloading the texlive package and following the installation instructions (https://www.tug.org/texlive/)\n\n";
    }
    print "Rerun this script once latex has been added to the default search path (./rp_config)\n\n";
    print "---------------------------------------\n";
    print "there are also detailed instructions in the README in the dependency directory\n";
    exit;
#    print "sleeping now, should exit later\n";
#    print "---------------------------------------\n";
#    sleep (3);
#    exit;
}

### Make sure all perl packages are installed
### JG addition -- wrote this block before I saw you added something similar above
#if ($clusters{broad} == 1){
#    unless (exists $ENV{rp_perlpackages}) {
#        print "Run the following commands to add rp_perlpackages as an environmental variable:\n";
#        print "echo \"export rp_perlpackages=/home/unix/sripke/perl_modules/\" >> ~/.my.bashrc\n";
#        print "echo \"setenv rp_perlpackages /home/unix/sripke/perl_modules/\" >> ~/.my.cshrc\n";
#        if ($shell eq "bash") {
#            print "export rp_perlpackages=/home/unix/sripke/perl_modules/\n";            
#        }
#        if ($shell eq "tcsh") {
#            print "setenv rp_perlpackages /home/unix/sripke/perl_modules/\n";
#        }

#        print "./rp_config\n\n";
#        exit;
#    }
#    else { print "Detected rp_perlpackages as an environmental variable.\n\n";}
#}
if ($clusters{genomedk} == 1){
    unless (exists $ENV{rp_perlpackages}) {
        print "Run the following commands to add rp_perlpackages as an environmental variable:\n";
        print "echo \"export rp_perlpackages=/project/ricopili/perl_packages/\" >> ~/.bashrc\n";
        print "export rp_perlpackages=/project/ricopili/perl_packages/\n";
        print "./rp_config\n\n";
        exit;
    }
    else { print "Detected rp_perlpackages as an environmental variable.\n\n";}
}
if ($clusters{mssm} == 1){
    unless (exists $ENV{rp_perlpackages}) {
        print "Run the following commands to add rp_perlpackages as an environmental variable:\n";
        print "echo \"export rp_perlpackages=/hpc/users/xripkes01/perl_modules/\" >> ~/.bashrc\n";
        print "export rp_perlpackages=/hpc/users/xripkes01/perl_modules/\n";
        print "./rp_config\n\n";
        exit;
    }
    else { print "Detected rp_perlpackages as an environmental variable.\n\n";}
}
if ($clusters{bih_qsub} == 1){
    unless (exists $ENV{rp_perlpackages}) {
        print "Run the following commands to add rp_perlpackages as an environmental variable:\n";
        print "echo \"export rp_perlpackages=/fast/users/panagigm_c/rp_bin/Statistics/\" >> ~/.bashrc\n";
        print "export rp_perlpackages=/fast/users/panagigm_c/rp_bin/Statistics/\n";
        print "./rp_config\n\n";
        exit;
    }
    else { print "Detected rp_perlpackages as an environmental variable.\n\n";}
}



if ($clusters{unc_slurm} == 1){
    unless (exists $ENV{rp_perlpackages}) {
        print "Run the following commands to add rp_perlpackages as an environmental variable:\n";
        print "echo \"export rp_perlpackages=/PATH_TO_PERLMODULES/\" >> ~/.bashrc\n";
        print "export rp_perlpackages=/PATH_TO_PERLMUODULES/\n";
        print "./rp_config\n\n";
        exit;
    }
    else { print "Detected rp_perlpackages as an environmental variable.\n\n";}
}




if ($clusters{custom} == 1){

#    print  "path2perl:".$path_to_perlmodules."\n";
#    sleep(10);
    unless (exists $ENV{rp_perlpackages}) {
        print "Run the following commands to add rp_perlpackages as an environmental variable:\n";
        print "echo \"export rp_perlpackages=$path_to_perlmodules\" >> ~/.bashrc\n";
        print "export rp_perlpackages=$path_to_perlmodules\n";
        print "./rp_config\n\n";
        exit;
    }
    else { print "Detected rp_perlpackages as an environmental variable.\n\n";}

    unless (exists $ENV{RPHOME}) {
        print "Run the following commands to add RPHOME as an environmental variable:\n";
        print "echo \"export RPHOME=$rphome\" >> ~/.bashrc\n";
        print "export RPHOME=$rphome\n";
        print "./rp_config\n\n";
        exit;
    }
    else { print "Detected RPHOME as an environmental variable.\n\n";}
    
}



### Make sure lapack is installed
if ($clusters{genomedk} == 1){
    unless ($ENV{EXTRAS} =~ /lapack/) {
        print "Run the following commands to add lapack to the default search path:\n";
        print "echo \"source /com/extra/lapack/3.5.0/load.sh\" >> ~/.bashrc\n";
        print "source /com/extra/lapack/3.5.0/load.sh\n";
        print "./rp_config\n\n";
        exit;
    }
    else { print "Detected lapack is installed.\n\n";}
}



my $ans_ow = "y";

my $old_initials = "NA";
my $old_email = "NA";

if (-e $conf_file) {
    print "*************************************************************\n";
    print "Configuration file already exists at $conf_file\n";
    print "Do you wish to build a new version of this file (with default values)? (y/n)\n";
    print "        - if yes, a backup of the present file will be here: $conf_file.copy - \n";
    print "        - if not, then present $conf_file will be fully reused (choose this for simple update installation in the same environment) - \n";
    while (1) {
        $ans_ow = lc <>;
        chomp $ans_ow;
        if ($ans_ow eq "y") {


	    my @tmp_lines = `grep ^init $conf_file`;
	    my @cells = split /\s+/, $tmp_lines[0];
	    $old_initials = $cells[1];
	    my @tmp_lines = `grep ^email $conf_file`;
	    my @cells = split /\s+/, $tmp_lines[0];
	    $old_email = $cells[1];	    


			    
            &mysystem("cp $conf_file $conf_file.copy");
            last;
        }
        elsif ($ans_ow eq "n") {print "Not overwriting $conf_file.\n";last;}
        else {print "Please answer with y or n.\n";}
    }
};



my $sloc = "";
my $loloc = "";
my $initials = "";
my $email = "";
my @text = ();

if ($ans_ow eq "y"){
#############################
# make scratch directory
#############################
if ($clusters{broad} == 1) {
    my $user_name = basename($ENV{HOME});
    $sloc = "/broad/hptmp/$user_name/";
    print "Do you want to use the following default scratch directory? (y or n)\n";
    print "\t$sloc\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {print "Using $sloc as the scratch directory.\n\n";last;}
        elsif ($answer eq "n") {print "Please enter a scratch directory to use:\n";
				$sloc = <>;
				chomp $sloc;
				$sloc =~ s/^~/$ENV{HOME}/g;
				$sloc =~ s/^\./$cdir/g;
				last;}
        else {print "Please answer with y or n.\n";}
    }
}
elsif ($clusters{lisa} == 1) {
    $sloc = "/scratch/";
    print "Do you want to use the following default scratch directory? (y or n)\n";
    print "\t$sloc\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {print "Using $sloc as the scratch directory.\n\n";last;}
        elsif ($answer eq "n") {print "Please enter a scratch directory to use:\n";
				$sloc = <>;
				chomp $sloc;
				$sloc =~ s/^~/$ENV{HOME}/g;
				$sloc =~ s/^\./$cdir/g;        
				last;}
        else {print "Please answer with y or n.\n";}
    }
}

elsif ($clusters{computerome} == 1) {
    $sloc = "/scratch/";
    print "Do you want to use the following default scratch directory? (y or n)\n";
    print "\t$sloc\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {print "Using $sloc as the scratch directory.\n\n";last;}
        elsif ($answer eq "n") {print "Please enter a scratch directory to use:\n";
				$sloc = <>;
				chomp $sloc;
				$sloc =~ s/^~/$ENV{HOME}/g;
				$sloc =~ s/^\./$cdir/g;        
				last;}
        else {print "Please answer with y or n.\n";}
    }
}

elsif ($clusters{co_ipsych} == 1) {
    $sloc = "/data/scratch/";
    print "Do you want to use the following default scratch directory? (y or n)\n";
    print "\t$sloc\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {print "Using $sloc as the scratch directory.\n\n";last;}
        elsif ($answer eq "n") {print "Please enter a scratch directory to use:\n";
				$sloc = <>;
				chomp $sloc;
				$sloc =~ s/^~/$ENV{HOME}/g;
				$sloc =~ s/^\./$cdir/g;        
				last;}
        else {print "Please answer with y or n.\n";}
    }
}

elsif ($clusters{genomedk} == 1) {
    $sloc = "/project/ricopili/scratch_dir/";
    print "Do you want to use the following default scratch directory? (y or n)\n";
    print "\t$sloc\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {print "Using $sloc as the scratch directory.\n\n";last;}
        elsif ($answer eq "n") {print "Please enter a scratch directory to use:\n";
				$sloc = <>;
				chomp $sloc;
				$sloc =~ s/^~/$ENV{HOME}/g;
				$sloc =~ s/^\./$cdir/g;        
				last;}
        else {print "Please answer with y or n.\n";}
    }
}


elsif ($clusters{mssm} == 1) {
    my $user_name = $ENV{USER};
    $sloc = "/scratch/$user_name/";
    print "Do you want to use the following default scratch directory? (y or n)\n";
    print "\t$sloc\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {print "Using $sloc as the scratch directory.\n\n";last;}
        elsif ($answer eq "n") {print "Please enter a scratch directory to use:\n";
				$sloc = <>;
				chomp $sloc;
				$sloc =~ s/^~/$ENV{HOME}/g;
				$sloc =~ s/^\./$cdir/g;        
				last;}
        else {print "Please answer with y or n.\n";}
    }
}

elsif ($clusters{bih_qsub} == 1) {
    my $user_name = $ENV{USER};
    $sloc = "$home/scratch/";
    print "Do you want to use the following default scratch directory? (y or n)\n";
    print "\t$sloc\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {print "Using $sloc as the scratch directory.\n\n";last;}
        elsif ($answer eq "n") {print "Please enter a scratch directory to use:\n";
				$sloc = <>;
				chomp $sloc;
				$sloc =~ s/^~/$ENV{HOME}/g;
				$sloc =~ s/^\./$cdir/g;        
				last;}
        else {print "Please answer with y or n.\n";}
    }
}


elsif ($clusters{uppmax} == 1) {
    $sloc = "\$TMPDIR"; # $TMPDIR gets populated with /scratch/$SLURM_JOB_ID for
                        # each job. Storing files directly in /scratch is not safe.
                        # On login nodes $TMPDIR is just /scratch/.
    print "Do you want to use the following default scratch directory? (y or n)\n";
    print "\t$sloc\n";
    while (1) {
        my $answer = lc <>;
        chomp $answer;
        if ($answer eq "y") {print "Using $sloc as the scratch directory.\n\n";last;}
        elsif ($answer eq "n") {print "Please enter a scratch directory to use:\n";
				$sloc = <>;
				chomp $sloc;
				last;}
        else {print "Please answer with y or n.\n";}
    }
}

elsif ($clusters{custom} == 1) {
    $sloc = $conf{"path_to_scratchdir"};
    if ($sloc eq "") {
	print "Error: <path_to_scratchdir> is not set in $rp_custom_installation_file\n";
	exit;
    }
    print "Using the following default scratch directory:\n";
    print "\t$sloc\n";
}


else {
    print "Please enter a scratch directory to use:\n";
    $sloc = <>;
    chomp $sloc;
    while (1) {
	print "Using $sloc as the scratch directory.\n\n";
    }
}

#unless (-d $sloc) {
#    print "Making scratch directory: $sloc\n\n";
#    &mysystem("mkdir -p $sloc");
#}
#else {
#    print "Scratch directory already exists at $sloc\n";
#}
print "\n";




#############################
# rewrite scratchdir for pfdjam
#############################



#    print "$cdir/pdfjam\n";

#die $!."($cdir/pdfjam/pdfjam)" unless open FILE, "< $cdir/pdfjam/pdfjam";
#die $!."($cdir/pdfjam/pdfjam.ow)" unless open OUT, "> $cdir/pdfjam/pdfjam.ow";
#while (my $line = <FILE>){
#    $line =~ s!/psych/genetics_data/ricopili_tmp!$sloc!;   ################## needs to be changed SRIPKE
#    print OUT "$line";
#}
#close FILE;
#close OUT;
#system ("mv $cdir/pdfjam/pdfjam.ow $cdir/pdfjam/pdfjam");
#system ("chmod a+x $cdir/pdfjam/pdfjam");
#print "rewrote $cdir/pdfjam/pdfjam with scratchdir\n";
    


#############################
# rewrite Utils.pm
#############################


#    print "$cdir/pdfjam\n";

if (0) {
    die $!."($cdir/Ricopili/Utils.pm)" unless open FILE, "< $cdir/Ricopili/Utils.pm";
    die $!."($cdir/Ricopili/Utils.pm.ow)" unless open OUT, "> $cdir/Ricopili/Utils.pm.ow";
    while (my $line = <FILE>){
	$line =~ s!RPHOME!$rphome!;   ################## needs to be changed SRIPKE
	print OUT "$line";
    }
    close FILE;
    close OUT;
    system ("mv $cdir/Ricopili/Utils.pm.ow $cdir/Ricopili/Utils.pm");
    system ("chmod a+x $cdir/Ricopili/Utils.pm");
    print "rewrote RPHOME $cdir/Ricopili/Utils.pm with scratchdir\n";
}



#############################
# get initials from custom, old config file or user
#############################
if ($clusters{custom}){
    $initials = $conf{"rp_user_initials"};
    if ($initials eq "") {
	print "Error: <rp_user_initials> is not set in $rp_custom_installation_file\n";
	exit;
    } 

}
elsif ($old_initials ne "NA") {
    print " -> Do you want to use the initials found in the old $conf_file? ($old_initials) (y or n)\n";
    while (1) {
	my $answer = lc <>;
	chomp $answer;
	if ($answer eq "y") {$initials = $old_initials;last;}
	elsif ($answer eq "n") {
	    print "please give me new ones then: \n";
	    while (1) {
		$initials = lc <>;
		chomp $initials;
		if (length($initials) == 2) {last;}
		else {print "Make sure initials are 2 letters!\n";}
	    }
	    
	    
	    last;
	}
	else {print "Please answer with y or n.\n";}
    }
}
else {
    print "Please enter your initials (2 letters):\n";
    while (1) {
	$initials = lc <>;
	chomp $initials;
	if (length($initials) == 2) {last;}
	else {print "Make sure initials are 2 letters!\n";}
    }
}
print "\n";



#############################
# get email from custom, old config file or user
#############################
if ($clusters{custom}){
    $email = $conf{"rp_user_email"};
    if ($email eq "") {
	print "Error: <rp_user_email> is not set in $rp_custom_installation_file\n";
	exit;
    } 

}

elsif ($old_email ne "NA") {
    print " -> Do you want to use the email found in the old $conf_file? ($old_email) (y or n)\n";
    while (1) {
	my $answer = lc <>;
	chomp $answer;
	if ($answer eq "y") {$email = $old_email;last;}
	elsif ($answer eq "n") {
	    print "please give me a new one then: \n";

	    while (1) {
		$email = lc <>;
		chomp $email;
		last;
	    }
	    
	    last;
	}
	else {print "Please answer with y or n.\n";}
    }
}
else {
    print " -> please enter your email address:\n";
    $email = <>;
    chomp $email;
}
print "\n";


my $defall = 0;

if ($clusters{lisa} == 1) {
    print "Do you want to use default values for the rest of the installation process? (y or n)\n";
    while (1) {
	my $answer = lc <>;
	chomp $answer;
	if ($answer eq "y") {print "Using default values for the rest of the installation process\n\n"; $defall = 1;last;}
	elsif ($answer eq "n") {print "Not using default values for the rest of the installation process\n\n"; $defall = 0;last;}
	else {print "Please answer with y or n.\n";}
    }
}





    
#############################
# set location for logfiles
#############################

if ($clusters{custom}){
    $loloc = $conf{"rp_logfiles"};
    if ($loloc eq "") {
	print "Error: <rp_logfiles> is not set in $rp_custom_installation_file\n";
	exit;
    } 
}
else {
    my $home_dir = $ENV{HOME};
    $loloc = "$home_dir/";
    print "Do you want to use the following default directory to store your log files ($loloc)? (y or n)\n";
    print "\t$loloc\n";
    if ($defall == 0) {
	while (1) {
	    my $answer = lc <>;
	    chomp $answer;
	    if ($answer eq "y") {print "Using $loloc as the log directory.\n\n";last;}
	    elsif ($answer eq "n") {print "Please enter a log directory to use:\n";
				    $loloc = <>;
				    chomp $loloc;
				    $loloc =~ s/^~/$ENV{HOME}/g;
				    $loloc =~ s/^\./$cdir/g;        
				    last;}
	    else {print "Please answer with y or n.\n";}
	}
    }
}



print "\n";

my %longvar = ("ploc","PLINK",
	       "p2loc","PLINK2",
	       "shloc","SHAPEIT",
	       "sh3loc","SHAPEIT3",
	       "ealoc","EAGLE",
	       "bgziploc","BGZIP",
	       "tabixloc","TABIX",
	       "minimac3loc","Minimac3",
	       
	       "i2loc","IMPUTE2",
	       "i4loc","IMPUTE4",
	       "liloc","Liftover",
	       "eloc","Eigenstrat",
	       "rloc","R",
	       "rpac","Rpackages",
	       "hmloc","HapMap reference",
	       "meloc","METAL",
	       "ldloc","LDscore",
	       "bcloc","BCFtools",
	       "bcrloc","BCFtools_resources",
#	       "hvloc","HaploView"
    );
	       

my %variables = ("ploc", "",
		 "p2loc","",
		 "bgziploc","",
		 "tabixloc","",
		 "minimac3loc","",
		 
		 "shloc","",
		 "sh3loc","",
		 "ealoc","",
		 "i2loc","",
		 "i4loc","",
		  "liloc","",
		  "eloc","",
		  "rloc","",
		 "rpac","",
		  "hmloc","",
		 "meloc","",
		 "bcloc","",
		 "bcrloc","",
#		  "hvloc","",
    );




    
if ($clusters{broad}){
    %variables = ("ploc", "/home/unix/sripke/plink_src/src/",
		  "p2loc","/home/unix/sripke/plink_src/plink_1.9_newest/",
		  "shloc","/home/unix/sripke/shapeit/",
		  "sh3loc","/psych/genetics_data/ripke/rp_bins/shapeit3/",
		  "bgziploc","/psych/genetics_data/ripke/rp_bins/tabix/tabix_rom/",
		  "tabixloc","/psych/genetics_data/ripke/rp_bins/tabix/tabix_rom/",
		  "minimac3loc","/psych/genetics_data/ripke/rp_bins/tabix/tabix_rom/",
		  "ealoc","/psych/genetics_data/ripke/rp_bins/Eagle_v2.3.5/",
		  "i2loc","/psych/genetics_data/ripke/references_from_debakkerscratch/impute_v2/impute_v2/impute_v2.3.2_x86_64_static/",
		  "i4loc","/psych/genetics_data/ripke/rp_bins/impute_v4/",
		  "liloc","/home/unix/sripke/liftover/",
		  "eloc","/home/unix/sripke/EIG6.0beta/bin/",
		  "ldloc","/psych/genetics_data/ripke/ldsc/",
		  "rloc","broadinstitute",
		  "rpac","NA",
		  "hmloc","/psych/genetics_data/ripke/references_outdated/hapmap_ref/",
		  "meloc","/psych/genetics_data/ripke/references_from_debakkerscratch/metal/2011_03/",
		  "bcloc","/psych/genetics_data/ripke/rp_bins/bcftools/new_0816/bcftools-1.3.1_bin/bin/",
		  "bcrloc","/psych/genetics_data/ripke/rp_bins/bcftools/bcftools-1.3.1/resources/",
#		  "hvloc","/home/radon01/sripke/bakker_ripke/haploview/",
	);
}

elsif ($clusters{lisa}){
    %variables = ("ploc", "/home/gwas/plink/1.08/src",
		  "p2loc","/home/gwas/plink2/plink_1.9_newest",
		  "shloc","/home/gwas/shapeit",
		  "sh3loc","/home/gwas/shapeit/shapeit3",
		  "ealoc","/home/gwas/eagle/Eagle_v2.3.5/",
		  "bgziploc","/home/gwas/rp_exec/bgzip/",
		  "tabixloc","/home/gwas/rp_exec/tabix/",
		  "minimac3loc","/home/gwas/rp_exec/minimac/",
		  "i2loc","/home/gwas/bin_impute_v2/impute_v2.3.2_x86_64_static",
		  "i4loc","/home/gwas/bin_impute_v4",
		  "liloc","/home/gwas/liftover",
		  "ldloc","/home/gwas/ldsc/",
		  "eloc","/sara/sw/eigensoft-5.0.1/bin/",
		  "rloc","/sara/sw/R-3.1.2/bin/R",
		  "rpac","/home/gwas/Rlibs",
		  "hmloc","/home/gwas/pgc-samples/hapmap_ref/",
		  "meloc","/home/gwas/metal",
		  "bcloc","/home/gwas/bcftools/",
		  "bcrloc","/home/gwas/bcftools/",
#		  "hvloc","./",
	);
}



elsif ($clusters{computerome}){
    %variables = ("ploc", "/home/people/sripke/rp_external_bins/plink/",
		  "p2loc","/home/people/sripke/rp_external_bins/plink_1.9_newest/",
		  "shloc","/home/people/sripke/rp_external_bins/shapeit/",
		  "sh3loc","NA",
		  "ealoc","please_download_https://data.broadinstitute.org/alkesgroup/Eagle/downloads/",

		  
		  "i2loc","/home/people/sripke/rp_external_bins/impute2/",
		  "i4loc","NA",
		  "liloc","/home/people/sripke/rp_external_bins/liftover/",
		  "ldloc","/home/people/sripke/rp_external_bins/ldsc/",
		  "eloc","/home/people/sripke/rp_external_bins/EIG6.0beta/",
		  "rloc","/services/tools/R-3.1.2/bin/",
		  "rpac","/home/people/sripke/rp_external_bins/Rpackages/",
		  "hmloc","/home/people/sripke/imputation_references/",
		  "meloc","/home/people/sripke/rp_external_bins/metal/",
		  "bcloc","NA",
		  "bcrloc","NA",

		  "bgziploc","NA",
		  "tabixloc","NA",
		  "minimac3loc","NA",
#		  "hvloc","./",
	);
}


elsif ($clusters{co_ipsych}){
    %variables = ("ploc", "/data/tools/plink-1.07/",
		  "p2loc","/data/tools/plink2_sept2015/",
		  "shloc","/data/tools/shapeit_sept_2015/",
		  "sh3loc","NA",
		  "ealoc","please_download_https://data.broadinstitute.org/alkesgroup/Eagle/downloads/",
		  "i2loc","/data/tools/impute-2.3.2/",
		  "i4loc","NA",
		  "liloc","/data/user_tools/rp_external_bins/liftover/",
		  "ldloc","/data/user_tools/rp_external_bins/ldsc/",
		  "eloc","/data/tools/eigensoft-6.0.1/bin/",
		  "rloc","/data/tools/R-3.2.1/bin/",
		  "rpac","/data/user_tools/rp_external_bins/Rpackages/",
		  "hmloc","/data/user_tools/imputation_references/",
		  "meloc","/data/tools/metal-20110325/",
		  "bcloc","NA",
		  "bcrloc","NA",

		  "bgziploc","NA",
		  "tabixloc","NA",
		  "minimac3loc","NA",
#		  "hvloc","./",
	);
}

elsif ($clusters{genomedk}){
    %variables = ("ploc", "/project/ricopili/plink_src/",
		  "p2loc","/project/ricopili/plink_1.9_jul4/",
		  "shloc","/project/ricopili/3rd_bins/shapeit/",
		  "sh3loc","NA",
		  "ealoc","please_download_https://data.broadinstitute.org/alkesgroup/Eagle/downloads/",
		  "i2loc","/project/ricopili/3rd_bins/impute2/",
		  "i4loc","NA",
		  "liloc","/project/ricopili/3rd_bins/liftover/",
		  "eloc","/project/ricopili/3rd_bins/eigenstrat/bin/",
		  "rloc","/com/extra/R/3.1.0/bin",
		  "rpac","NA",
		  "hmloc","/project/ricopili/reference_dir/",
		  "meloc","/project/ricopili/3rd_bins/metal/",
		  "bcloc","NA",
		  "bcrloc","NA",

		  "bgziploc","NA",
		  "tabixloc","NA",
		  "minimac3loc","NA",
#		  "hvloc","./",
	);
}

elsif ($clusters{mssm}){
    %variables = ("ploc", "/hpc/users/xripkes01/ricopili/3rd_binaries/plink-1.07-src-sripke/",
		  "p2loc","/hpc/users/xripkes01/ricopili/3rd_binaries/plink-1.09-src-aug4/",
		  "shloc","/hpc/users/xripkes01/ricopili/3rd_binaries/shapeit/",
		  "sh3loc","NA",
		  "ealoc","pleasedownload_https://data.broadinstitute.org/alkesgroup/Eagle/downloads/",
		  "i2loc","/hpc/users/xripkes01/ricopili/3rd_binaries/impute2/",
		  "i4loc","NA",
		  "liloc","/hpc/users/xripkes01/ricopili/3rd_binaries/liftover/",
		  "eloc","/hpc/packages/minerva-common/eigensoft/5.0.1/bin/",
		  "rloc","/hpc/packages/minerva-common/R/2.15.3/lib64/R/bin/",
		  "rpac","NA",
		  "hmloc","/hpc/users/xripkes01/ricopili/reference_dir/",
		  "meloc","/hpc/users/xripkes01/ricopili/3rd_binaries/metal/",
		  "bcloc","NA",
		  "bcrloc","NA",

		  "bgziploc","NA",
		  "tabixloc","NA",
		  "minimac3loc","NA",
#		  "hvloc","./",
	);
}

elsif ($clusters{bih_qsub}){
    my $dependency_dir = "$home/Ricopili_Dependencies";
    %variables = (
		  "p2loc","$dependency_dir/plink",

	"sh3loc","$dependency_dir/shapeit3",
	"shloc","$dependency_dir/shapeit",
		  "ealoc","$dependency_dir/eagle",
		  "i2loc","$dependency_dir/impute_v2",
		  "i4loc","$dependency_dir/impute_v4",
		  "liloc","$dependency_dir/liftover/",
		  "eloc","$dependency_dir/eigensoft/EIG-6.1.4/bin/",
		  "rloc","$home/local/R/bin/",  ## separate dir
		  "rpac","/fast/users/panagigm_c/local/R/lib/R/library/rmeta", ## separate dir
		  "hmloc","$dependency_dir/hapmap_ref/",
		  "meloc","$dependency_dir/metal/",
		  "bcloc","$dependency_dir/bcftools/bcftools-1.3.1_bin/bin/",
		  "bcrloc","$dependency_dir/bcftools/bcftools-1.3.1/resources/",

		  "bgziploc","$dependency_dir/tabix",
		  "tabixloc","$dependency_dir/tabix/",
		  "minimac3loc","$dependency_dir/tabix/",
#		  "hvloc","./",
	);
}

elsif ($clusters{unc_slurm}){
    my $rp_dependencies_dir = "/nas/depts/007/sullilab/projects/ppd_sig/Ricopili_Dependencies/";
    %variables = (

	"p2loc","$rp_dependencies_dir/plink",

	"sh3loc","$rp_dependencies_dir/shapeit3",
	"shloc","$rp_dependencies_dir/shapeit",
	"ealoc","$rp_dependencies_dir/eagle",
	"i2loc","$rp_dependencies_dir/impute_v2",
	"i4loc","$rp_dependencies_dir/impute_v4",
	"liloc","$rp_dependencies_dir/liftover/",
	"eloc","$rp_dependencies_dir/eigensoft/EIG-6.1.4/bin/",
	"rloc","module_SPACE_load_SPACE_r_SPACE_;_SPACE_R",  ## separate dir
	"rpac","/nas/depts/007/sullilab/projects/ppd_sig/Rpackages/3.3/", ## separate dir
	"hmloc","$rp_dependencies_dir/hapmap_ref/",
	"meloc","$rp_dependencies_dir/metal/",
	"bcloc","$rp_dependencies_dir/bcftools/bcftools-1.3.1_bin/bin/",
	"bcrloc","$rp_dependencies_dir/bcftools/bcftools-1.3.1/resources/",
	"ldloc","$rp_dependencies_dir/ldsc/",
	
	"bgziploc","$rp_dependencies_dir/tabix",
	"tabixloc","$rp_dependencies_dir/tabix/",
	"minimac3loc","$rp_dependencies_dir/tabix/",

	);
}

elsif ($clusters{custom}){
    my $rp_dependencies_dir = $conf{"rp_dependencies_dir"};
    if ($rp_dependencies_dir eq "") {
	print "Error: <rp_dependencies_dir> is not set in $rp_custom_installation_file\n";
	exit;
    }
    my $starting_R = $conf{"starting_R"};
    if ($starting_R eq "") {
	print "Error: <starting_R> is not set in $rp_custom_installation_file\n";
	exit;
    }
    my $R_packages_dir = $conf{"R_packages_dir"};
    if ($R_packages_dir eq "") {
	print "Error: <R_packages_dir> is not set in $rp_custom_installation_file\n";
	exit;
    }
    my $starting_ldsc = $conf{"starting_ldsc"};
    if ($starting_ldsc eq "") {
	print "Error: <starting_ldsc> is not set in $rp_custom_installation_file\n";
	exit;
    }
    my $ldsc_reference = $conf{"ldsc_reference"};
    if ($ldsc_reference eq "") {
	print "Error: <ldsc_reference> is not set in $rp_custom_installation_file\n";
	exit;
    }    

    
    %variables = (

	"p2loc","$rp_dependencies_dir/plink",
	"sh3loc","$rp_dependencies_dir/shapeit3",
	"shloc","$rp_dependencies_dir/shapeit",
	"ealoc","$rp_dependencies_dir/eagle",
	"i2loc","$rp_dependencies_dir/impute_v2",
	"i4loc","$rp_dependencies_dir/impute_v4",
	"liloc","$rp_dependencies_dir/liftover/",
	"eloc","$rp_dependencies_dir/eigensoft/EIG-6.1.4/bin/",
	"hmloc","$rp_dependencies_dir/hapmap_ref/",
	"meloc","$rp_dependencies_dir/metal/",
	
	"bcloc","$rp_dependencies_dir/bcftools/bcftools-1.9_bin/",
	"bcrloc","$rp_dependencies_dir/bcftools/resources/",

#	"bcloc","$rp_dependencies_dir/bcftools/bcftools-1.3.1_bin/bin/",
#	"bcrloc","$rp_dependencies_dir/bcftools/bcftools-1.3.1/resources/",
	
	"bgziploc","$rp_dependencies_dir/bgzip/",
	"tabixloc","$rp_dependencies_dir/tabix/",
	"minimac3loc","$rp_dependencies_dir/Minimac3/",
	"ldsc_start","$starting_ldsc",
	"ldsc_ref","$ldsc_reference",

	"rloc","$starting_R",  ## separate dir
	"rpac","$R_packages_dir", ## separate dir
	);

    unless (-d "$rp_dependencies_dir/Minimac3/") {
	$variables{"minimac3loc"} = "$rp_dependencies_dir/tabix";
	print "*************************************************************************\n";
	print "         ($rp_dependencies_dir/tabix)\n";
	print "Warning, using old directory structure, please update Dependency Download\n";
	print "                       or use an updated custom-file\n";
	print "*************************************************************************\n";
	sleep (3);
    }
    unless (-d "$rp_dependencies_dir/bgzip/") {
	$variables{"bgziploc"} = "$rp_dependencies_dir/tabix";
	print "*************************************************************************\n";
	print "         ($rp_dependencies_dir/tabix)\n";
	print "Warning, using old directory structure, please update Dependency Download\n";
	print "                       or use an updated custom-file\n";
	print "*************************************************************************\n";
	sleep (3);
    }
    unless (-d "$rp_dependencies_dir/bcftools/bcftools-1.9_bin/") {
	$variables{"bcloc"} = "$rp_dependencies_dir/bcftools/bcftools-1.3.1_bin/bin/";
	print "*************************************************************************\n";
	print "         ($rp_dependencies_dir/bcftools/bcftools-1.3.1_bin/bin/)\n";
	print "Warning, using old directory structure, please update Dependency Download\n";
	print "                       or use an updated custom-file\n";
	print "*************************************************************************\n";
	sleep (3);
    }
    unless (-d "$rp_dependencies_dir/bcftools/resources/") {
	$variables{"bcrloc"} = "$rp_dependencies_dir/bcftools/bcftools-1.3.1/resources/";
	print "*************************************************************************\n";
	print "         ($rp_dependencies_dir/bcftools/bcftools-1.3.1/resources)\n";
	print "Warning, using old directory structure, please update Dependency Download\n";
	print "                       or use an updated custom-file\n";
	print "*************************************************************************\n";
	sleep (3);
    }

    
    

    
}

elsif ($clusters{uppmax}){
    %variables = ("ploc", "/sw/apps/bioinfo/plink/1.07/$uppmax_cluster/",
		  "p2loc","/proj/$uppmax_project/ricopili/software/plink2/",
		  "shloc","/proj/$uppmax_project/ricopili/software/shapeit/bin/",
		  "sh3loc","NA",
		  "ealoc","please_download_https://data.broadinstitute.org/alkesgroup/Eagle/downloads/",
		  "i2loc","/proj/$uppmax_project/ricopili/software/impute2/impute_v2.3.2_x86_64_static/",
		  "i4loc","NA",
		  "liloc","/proj/$uppmax_project/ricopili/software/liftover/",
		  "ldloc","/proj/$uppmax_project/ricopili/software/ldsc/",
		  "eloc","/proj/$uppmax_project/ricopili/software/EIG6.0.1/bin/",
		  "rloc","/usr/bin/",
		  "rpac","/proj/$uppmax_project/ricopili/software/Rpackages",
		  "hmloc","/proj/$uppmax_project/ricopili/hapmap_ref/",
		  "meloc","/proj/$uppmax_project/ricopili/software/metal/generic-metal/",
		  "bcloc","NA",
		  "bcrloc","NA",
		  
		  "bgziploc","NA",
		  "tabixloc","NA",
		  "minimac3loc","NA",
    	);
}


unless ($clusters{custom}){
    foreach (keys %variables){

	if ($variables{$_} eq "broadinstitute" && $longvar{$_} eq "R") {
	    print "You are running R on broad, took the default value\n\n";
	}
	elsif ($variables{$_} eq "NA" && $longvar{$_} eq "Rpackages") {
	    print "assuming library rmeta is installed on standard R\n\n";
	}
	else {
	    if ($variables{$_} ne '' && (-d $variables{$_})){
		print "For $_($longvar{$_}), do you want to use the default location ($variables{$_}) (y or n)?\n";
		if ($defall == 0) {
		    while (1) {
			my $answer = lc <>;
			chomp $answer;
			if ($answer eq "y") {
			    print "Using $variables{$_} for $longvar{$_}.\n\n";
			    last;
			}
			elsif ($answer eq "n") {print "Please enter a new location to use for $longvar{$_}:\n";
						my $input = <>;
						chomp $input;
						$input =~ s/^~/$ENV{HOME}/g;
						$input =~ s/^\./$cdir/g;
						unless ( -d $input ){print "Not a valid directory. Please try again.\n";next;}
						print "\n";
						last;}
			else {print "Please answer with y or n.\n";}
		    }
		}
		else {
		    print " - took default value -\n";
		}
	    }
	    else {
		while (1){
		    print "For $_($longvar{$_}), no default value found, right now it is this here: <$variables{$_}> (y or n)?\n";
		    my $input = "";
		    $input = <>;
		    chomp $input;
		    $input =~ s/^~/$ENV{HOME}/g;
		    $input =~ s/^\./$cdir/g;
		    unless ( -d $input ){print "Not a valid directory. Please try again.\n";next;}
		    $variables{$_} = $input;
		    print "\n";
		    last;
		}
	    }
	}
    }
}


foreach (keys %variables){
    push (@text, "$_ $variables{$_}");
}

push (@text, "home $home");
push (@text, "sloc $sloc");
push (@text, "init $initials");
push (@text, "email $email");
push (@text, "loloc $loloc");



my @batch_variables= qw /batch_jobcommand batch_name batch_jobfile batch_memory_request batch_walltime batch_array batch_stdout batch_stderr batch_job_dependency batch_array_task_id batch_max_parallel_jobs_per_one_array batch_other_job_flags batch_job_output_jid batch_ncores_per_node batch_mem_per_node/;

if ($clusters{custom}){
    foreach my $bv (@batch_variables) {
	if ($conf{$bv} eq "") {
	    print "Error: <$bv> is not set in $rp_custom_installation_file\n";
	    exit;
	}
	push (@text, "$bv $conf{$bv}");
    }
}


### define queue depending on cluster
#if ($clusters{broad}){push (@text, "queue bsub")}

if ($clusters{broad}){push (@text, "queue qsub_b")}
if ($clusters{lisa}){push (@text, "queue qsub")}
if ($clusters{computerome} || $clusters{co_ipsych}){push (@text, "queue qsub_c")}
if ($clusters{genomedk}){push (@text, "queue slurm")}
if ($clusters{mssm}){push (@text, "queue msub")}
if ($clusters{unc_slurm}){push (@text, "queue unc_slurm")}
if ($clusters{custom}){push (@text, "queue custom")}
if ($clusters{bih_qsub}){push (@text, "queue bih_qsub")}
if ($clusters{uppmax}){push (@text, "queue slurm_u")}
if ($clusters{uppmax}){push (@text, "uppmax_project $uppmax_project")}
}

unless ( -e $conf_file && $ans_ow eq "n") {
    die $! unless open FILE, "> $conf_file";
    foreach (@text) {print FILE "$_\n"};
    close FILE;
}

#############################
# read ricopili.config file with default parameters
#############################
my %conf = (); ## hash with config parameters

### Read config file
die $!."($conf_file)" unless open FILE, "< $conf_file";
while (my $line = <FILE>){
    my @cells = split /\s+/, $line;
    $conf{$cells[0]} = $cells[1];
}
close FILE;

print "\n";

#############################
# write pipeline status file to home directory
#############################

my @log_file = ("$conf{loloc}/preimp_dir_info","$conf{loloc}/impute_dir_info","$conf{loloc}/pcaer_info","$conf{loloc}/idtager_info","$conf{loloc}/repqc2_info","$conf{loloc}/areator_info","$conf{loloc}/merge_caller_info","$conf{loloc}/postimp_navi_info","$conf{loloc}/reference_dir_info","$conf{loloc}/test_info","$conf{loloc}/clumper_info");

foreach (@log_file) {
    unless ( -e $_) {
    print "Creating pipeline status file to $_\n";
    &mysystem("touch $_");
    }
}

############################
# check whether all binary directories exist
############################
my @fail_path = ();
my %locs = ("ploc","","p2loc","","shloc","","sh3loc","","ealoc","","i2loc","","i4loc","","liloc","","eloc","","hmloc","","meloc","","rpac","bcloc", "bcrloc");

die $!."($conf_file)" unless open FILE, "< $conf_file";
while (my $line = <FILE>){
    my @cells = split /\s+/, $line;
    my $path = $cells[1];
    my $variable = $cells[0];
    unless (-d $path) {
        if (exists $locs{$variable}) {push(@fail_path,$variable)};
    }
}
close FILE;

#############################
# print finish statement
#############################

my $fail = 0;
if ($#fail_path != -1) { 

   
#    foreach (@fail_path) {
#        unless ($_ eq "rloc" && $clusters{broad} == 1) {

    foreach my $confvar (@fail_path) {
	if ($confvar eq "rloc" && $clusters{broad} == 1) {
            next;
	}
	elsif ($confvar eq "rpac" && $clusters{lisa} != 1) {
            next;
	}
	else{
            $fail += 1;
	    print "Error: $confvar not existing or missing permissions\n";
        }
    }
    if ($fail != 0) {
	print "Error: something went wrong (see above)\n";
        print "You will need to install the binaries as described here (https://sites.google.com/a/broadinstitute.org/ricopili/resources) and use a text editor (emacs,vim,etc.) to edit the file paths listed in $home/ricopili.conf for the following variables:\n";
	print "if already installed, the permissions might exclude you\n";
        foreach (@fail_path) {
            unless ($_ eq "rloc" && $clusters{broad} == 1) {
                print "\t$_\n";            
            }
        }
	exit;
    }
}


&mysystem("rm install_true");    
&mysystem("echo \"Configuration for RP was successful.\" | mail -s rp_config  $conf{'email'}");    



my $hostname = $ENV{HOSTNAME}.'.'.$ENV{DOMAINNAME};
if ($clusters{lisa} == 1) {
    $hostname = "lisa.surfsara.nl";
}
if ($clusters{computerome} == 1) {
    $hostname = "computerome.cbs.dtu.dk";
}

if ($clusters{co_ipsych} == 1) {
    $hostname = "ipsych.computerome.cbs.dtu.dk";
}


print "-------------------------------------------------------------------\n";
print "------------- here some tips        -------------------------------\n";
print "-------------------------------------------------------------------\n\n";
print "adding these commands to your ~/.bashrc can be very helpful(you have to logout and login again for these to be in effect)\n\n";
print "## for colored output of ls:\n";
print 'alias ls=\'ls --color=auto\''."\n\n";
print "## for easy copy over to your local machine:\n";
print 'alias c=\'sed "s#.*#scp '.$ENV{LOGNAME}.'@'.$hostname.':$(pwd)/& .#"\''."\n\n";


print "## for list of currently running jobs:\n";
if ($clusters{lisa} == 1 || $clusters{computerome} == 1 || $clusters{co_ipsych} == 1 || $clusters{broad} == 1) {
    print 'alias q=\'qstat -u '.$ENV{LOGNAME}."\'\n\n";
}
elsif ($clusters{uppmax}) {
    print 'alias q=\'squeue -u '.$username."\'\n\n";
}
else {
    print "alias q=\'bjobs -w\'\n\n";

}

if ($clusters{computerome} == 1) {
    print "## load queuing system by default:\n";
    print "module load torque\n\n";
    print "## different prompt:\n";
    print 'PS1="$USER@computerome.cbs.dtu.dk:"\'\w\'" "'."\n\n";      
}
elsif ($clusters{co_ipsych} == 1) {
    print "## different prompt:\n";
    print 'PS1="$USER@ipsych.computerome.cbs.dtu.dk:"\'\w\'" "'."\n\n";  
}
else {
    print "## different prompt:\n";
    print 'PS1="'.$ENV{USER}.'@'.$hostname.':"\'\w\'" "'."\n\n";
}



print "\n\n";
print "*********************************************************************\n";
print "*****  Installation successful                    *******************\n";
print "*********************************************************************\n";
print "*********************************************************************\n";
print "*********************************************************************\n";
print "*****  you should be able to use the pipeline as described        ***\n";
print "*****  if you want to use it from a different login:              ***\n";
print "*****      logout and relogin so that PATH is set correctly       ***\n";
print "*********************************************************************\n";
print "\n\n";
print "If you do not receive a success email with the subject rp_config, please check your email address is entered correctly at $conf_file\n\n";


exit;



########## Done ##########