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	<title><![CDATA[BOL: Write bash in perl script !]]></title>
	<link>https://bioinformaticsonline.com/snippets/view/42930/write-bash-in-perl-script?</link>
	<atom:link href="https://bioinformaticsonline.com/snippets/view/42930/write-bash-in-perl-script?" rel="self" type="application/rss+xml" />
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/snippets/view/42930/write-bash-in-perl-script</guid>
	<pubDate>Wed, 03 Mar 2021 22:48:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/snippets/view/42930/write-bash-in-perl-script</link>
	<title><![CDATA[Write bash in perl script !]]></title>
	<description><![CDATA[<code>#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 = (
    &#039;Cwd&#039;,
    &#039;File::chdir&#039;,
    &#039;File::Copy&#039;,
    &#039;POSIX&#039;,
    &#039;Tie::File&#039;,
    &#039;Try::Tiny&#039;,
    &#039;Data::Dumper&#039;,
    &#039;File::Basename&#039;,
    &#039;Bio::SeqIO&#039;,
    &#039;FindBin&#039;,
    &#039;File::Remove&#039;,
    &#039;Capture::Tiny&#039;,
    &#039;File::Temp&#039;,
    &#039;File::Spec::Functions&#039;,
    &#039;Statistics::Multtest&#039;,
    &#039;File::Path&#039;,
    &#039;Statistics::Distributions&#039;,
    &#039;Getopt::Long&#039;,
    &#039;Statistics::R&#039;,
    &#039;Math::Round&#039;,
    &#039;File::Find&#039;,
    &#039;Bio::DB::Taxonomy&#039;,
    &#039;Pod::Usage&#039;,
        );

    my ($inst) = ExtUtils::Installed-&gt;new();
    my (@installed_modules) = $inst-&gt;modules();

    for ( @import_modules ) {

        eval{ $inst-&gt;validate($_) };
        if($@) {
            print qq{\n Module $_   NOT OK!\n };
            #exit 1;
        } # end &#039;if&#039;
        else { print &quot;\n Module $_ OK!\n&quot;;}
    } # end &#039;for&#039;
} # end &#039;BEGIN&#039; block

#Bash script else here

print &quot;\nDownloading third party database for Alienomics\n&quot;;



print &lt;&lt; `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 &quot;----&quot;;
echo &quot;Jit here&quot;;
sleep 9s


#wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz;
echo &quot;JJ&quot;
EOC</code>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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