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";
#Install NCBI taxdump
my $url = 'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz';
my $file = 'taxdump.tar.gz';
my $code = getstore($url, $file);
#print $code;
my $ae = Archive::Extract->new( archive => $file);
my $ok = $ae->extract( to => 'third_party_DB/taxdump' );
#Install silvaDB
#https://www.arb-silva.de/no_cache/download/archive/release_138_1/Exports/
#LSU: Large subunit (23S/28S ribosomal RNAs)
#SSU: Small subunit (16S/18S ribosomal RNAs)
my $silva_url_LSU = 'https://www.arb-silva.de/fileadmin/silva_databases/release_138_1/Exports/SILVA_138.1_LSUParc_tax_silva.fasta.gz';
my $silva_LSU_fileName = 'SILVA_138.1_LSUParc_tax_silva.fasta.gz';
my $silva_LSU_code = getstore($silva_url_LSU, $silva_LSU_fileName);
#print $silva_LSU_code;
my $silva_LSU_ae = Archive::Extract->new( archive => $silva_LSU_fileName);
my $silva_ok = $silva_LSU_ae->extract( to => 'third_party_DB/silvaDB/SILVA_138.1_LSUParc_tax_silva.fasta' );
#Install buscoDB
#https://busco-archive.ezlab.org/
my $busco_url_LSU = 'https://busco-archive.ezlab.org/datasets/metazoa_odb9.tar.gz';
my $busco_LSU_fileName = 'metazoa_odb9.tar.gz';
my $busco_LSU_code = getstore($busco_url_LSU, $busco_LSU_fileName);
#print $busco_LSU_code;
my $busco_LSU_ae = Archive::Extract->new( archive => $busco_LSU_fileName);
my $busco_ok = $busco_LSU_ae->extract( to => 'third_party_DB/' );
#Install diamondDB
__END__
# BlastDB download
my $result = `mkdir taxdump; cd taxdump; wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz; tar xzfp taxdump.tar.gz`;
parseResult ($result);
#do your magic here
sub parseResult {
system ($_[0]);
}
__END__
my $content = get("ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz");
die "Couldn't get it!" unless defined $content;
if (is_success(get("$content"))) {
print "Download started";
}
if [ ! -d "$PWD/blastDB" ]; then
if [ ! -d "$PWD/blastDB" ]; then
mkdir $PWD/blastDB
fi
cd $PWD/blastDB
wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz"
for a in nt.*.tar.gz; do tar xzf $a; done
#Out of the directory
cd ..
else
echo -e "exists \t blastDB, If not installed sucessfully, delete the folder and re-run it"
fi
echo -e "\nAll Done\n"
echo -e "\nInstall R package install.packages('Ckmeans.1d.dp') \n"
/;
