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mirdeep2 installation saying bowtie not found

Basically when I try to install mirdeep2 using

perl install.pl

it fails and says

bowtie-1.2.0-linux-x86.zip not found on server http://sourceforge.net/project/bowtie-bio/bowtie/.

Anyone know what to do to make it work? I'm pretty sure it has something to do with this part of the install.pl file, but I dont know how to edit if(not -d "bowtie-$bowtie_version"){

    print STDERR "Downloading bowtie $bowtie_version binaries\n\n";
    if($a =~ /Darwin/i){ ## download mac version
        $bowtie = "bowtie-$bowtie_version-macos-x86_64.zip";
    }elsif($a =~ /x86_64/i){
        $bowtie = "bowtie-$bowtie_version-linux-x86_64.zip";
    }else{
        $bowtie = "bowtie-$bowtie_version-src.zip";
    }

    if(not -f $bowtie){
    if(check("http://sourceforge.net/project/bowtie-bio/bowtie/$bowtie_version/$bowtie")){
    $err=system("$dtool http://sourceforge.net/project/bowtie-bio/bowtie/$bowtie_version/$bowtie $dopt");

    if($err){
        die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
    }
        }elsif(check("http://sourceforge.net/project/bowtie-bio/bowtie/old/$bowtie_version/$bowtie")){
    $err=system("$dtool http://sourceforge.net/project/bowtie-bio/bowtie/old/$bowtie_version/$bowtie $dopt");
    if($err){
        die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
    }

Thanks

mirdeep2
• 2,098 views • link
updated by Biostar Biostar • written by nathanielsaxe • nathanielsaxe

1 answer

Try downloading, installing and adding Bowtie to the PATH before you install miRdeep.

• 0 views • link
written by h.mon h.mon

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