build_rnaseq.pl

#!/usr/bin/env perl

use strict;
use File::Path;

umask(0022);

##########################################

die "Need to provide argument for install path: $!\n" if (scalar @ARGV < 1);

my $branch_name='rnaseq';
my $install_base=$ARGV[0];
my $ergatis_git_export_path='https://github.com/IGS/rnaseq-pipeline.git';	# This uses Git currently.  Others use SVN.

## this directory will be created.  If it exists already, it and everything under it
#   will be removed
my $tmp_area = "/tmp/build_${branch_name}";

##########################################

clear_export_area($tmp_area);
clear_install_area($install_base);

install_ergatis($install_base);

set_idgen_configuration($install_base);
print STDERR "DONE!!!... exiting\n";
exit(0);

sub clear_export_area {
    my $base = shift;
    
    rmtree($tmp_area);
    mkdir($tmp_area) || die "failed to create temp directory: $tmp_area";
}

sub clear_install_area {
    my $base = shift;

    for my $subdir ( qw( bin docs lib pipeline_templates) ) {
        rmtree("$base/$subdir");
    }
    
    for my $file ( qw( software.config CHANGELOG.md) ) {
        if ( -e "$base/$file" ) {
            unlink( "$base/$file" );
        }
    }
};

sub install_ergatis {
    my $base = shift;
    
    print STDERR "Cloning the repo $ergatis_git_export_path (branch $branch_name) into $base ...\n";
	# Git options
	# -b <name of branch>
	# -depth 1  (only get latest revision history - speeds up cloning)
	#
    my $cmd = "echo p | git clone -b $branch_name --depth 1 $ergatis_git_export_path $base";
    system($cmd);

	print STDERR "Removing .git related files ...\n";
	run_command("rm -rf $base/.git");

	print STDERR "Rearranging package-$branch_name files ...\n";
	# Move all package-lgtseek contents to parent dir, and merge core Ergatis lib files there
    run_command("mv $base/package-${branch_name}/* $base; mv $base/core/lib/perl5/Ergatis $base/lib/perl5/");

	# Create the wrapper scripts within the "bin" directory from the executable scripts
    print STDERR "Creating wrapper scripts ...\n";
	run_command("sh $base/core/create_wrappers.sh $base");

	# Lastly remove extraneous directories
	print STDERR "Removing useless directories ...\n";
	run_command("rm -rf $base/core; rm -rf $base/package-${branch_name}; rm $base/README.md");

}

sub run_command {
    my $cmd = shift;
    
    system($cmd);
    
    if ( $? == -1 ) {
        die "failed to execute command ($cmd): $!\n";
    } elsif ( $? & 127 ) {
         my $out = sprintf "command ($cmd): child died with signal %d, %s coredump\n",
                    ($? & 127),  ($? & 128) ? 'with' : 'without';
         die($out);
    }
}

sub set_idgen_configuration {
    my $base = shift;
    
	print STDERR "Changing default ID generation to IGS-style ID generation...\n";
    
	for my $conf_file ( "$base/lib/perl5/Ergatis/IdGenerator/Config.pm" ) {
    
        my $reset_permission_to = undef;
    
        if ( ! -w $conf_file ) {
            $reset_permission_to = (stat $conf_file)[2] & 07777;
            chmod(0644, $conf_file) || die "couldn't chmod $conf_file for writing";
        }
    
        my @lines = ();
    
        ## change $base/lib/perl5/Ergatis/IdGenerator/Config.pm
        open(my $cfh, $conf_file) || die "couldn't open $conf_file for reading";

        while ( my $line = <$cfh> ) {
        #    if ( $line !~ /^\#/ ) {
        #        $line =~ s/\:\:DefaultIdGenerator/\:\:IGSIdGenerator/g;
        #    }
            
            push @lines, $line;
        }

        close $cfh;
        
        ## now stomp it with our current content
        open(my $ofh, ">$conf_file") || die "couldn't open $conf_file for writing\n";
            print $ofh join('', @lines);
        close $ofh;
        
        if ( defined $reset_permission_to ) {
            chmod($reset_permission_to, $conf_file) || die "couldn't restore permissions on $conf_file (tried to set to $reset_permission_to)";
        }
    }
}