BOL: Write bash in perl script !

BioScripts
Jit
Write bash in perl script !

Write bash in perl script !

By Jit 1395 days ago

#use strict;
use warnings;
use ExtUtils::Installed;
use LWP::Simple;
use Archive::Extract;
#
# First, check if all the required modules have been installed in the system and download the mandatory database
#
BEGIN {
    my @import_modules = (
    'Cwd',
    'File::chdir',
    'File::Copy',
    'POSIX',
    'Tie::File',
    'Try::Tiny',
    'Data::Dumper',
    'File::Basename',
    'Bio::SeqIO',
    'FindBin',
    'File::Remove',
    'Capture::Tiny',
    'File::Temp',
    'File::Spec::Functions',
    'Statistics::Multtest',
    'File::Path',
    'Statistics::Distributions',
    'Getopt::Long',
    'Statistics::R',
    'Math::Round',
    'File::Find',
    'Bio::DB::Taxonomy',
    'Pod::Usage',
        );

    my ($inst) = ExtUtils::Installed->new();
    my (@installed_modules) = $inst->modules();

    for ( @import_modules ) {

        eval{ $inst->validate($_) };
        if($@) {
            print qq{\n Module $_   NOT OK!\n };
            #exit 1;
        } # end 'if'
        else { print "\n Module $_ OK!\n";}
    } # end 'for'
} # end 'BEGIN' block

#Bash script else here

print "\nDownloading third party database for Alienomics\n";



print << `EOC`; # execute command and get results
set -o xtrace
echo hi there;
#wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz;
echo "----";
echo "Jit here";
sleep 9s


#wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz;
echo "JJ"
EOC

BOL

Jit

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Write bash in perl script !