hamzakhanvit has asked for the wisdom of the Perl Monks concerning the following question:
I am getting the following error upon compilation of my blast.cgi program
XSLoader::load('Your::Module', $Your::Module::VERSION) at /usr/lib/perl5/5.8.8/i386-linux-thread-multi/XSLoader.pm line 25.
Compilation failed in require at /usr/lib/perl5/5.8.8/File/Temp.pm line 137.
BEGIN failed--compilation aborted at /usr/lib/perl5/5.8.8/File/Temp.pm line 137.
Compilation failed in require at blast.cgi line 5.
BEGIN failed--compilation aborted at blast.cgi line 5.
Please help me out.
#!/usr/bin/perl use strict; use warnings; use Adrian::Goodies ':dirs'; use File::Temp; use File::Spec::Functions; use Env::Path 'PATH'; PATH->Append(BLAST_BIN_DIR) if BLAST_BIN_DIR; #my %VALID_PROGS = (blastn => 'allnucl', tblastn => 'allnucl', tblastx + => 'allnucl', # blastp => 'allprot', blastx => 'allprot'); #my %VALID_DBS = (allnucl => 'allnucl', nucl => 'allnucl', allflanks = +> 'allnucl', # flanks => 'allnucl', allprot => 'allprot', prot => ' +allprot'); my $cgi = CGI->new(); my ($title, $prog, $db, $seq) = ($cgi->param('title') || "notitle" . t +ime(), $cgi->param('prog'), $cgi->param('db'), $cgi->param('sequence')); $title =~ s/\s/ /g; $title = "notitle" . time() if $title eq ''; $seq =~ s/[^A-Za-z]//g; if ($cgi->request_method() eq 'POST' #and exists $VALID_PROGS{$prog} a +nd #exists $VALID_DBS{$db} and $seq) { my $seqfile = File::Temp->new(); open (my $fh, '>', $seqfile); print $fh ">$title\n"; print $fh $seq, "\n"; close $fh; my $execstring; # currently is secure if ($prog eq "blastp" and $db eq "allnucl"){ $execstring = "/home/groupii/ncbi-blast/bin/$prog -db \"" . ca +tfile(BLAST_DB_DIR, "allprot") . "\" -max_target_seqs 10 -word_size 5 + -evalue 100 -query \"$seqfile\""; } elsif ($prog eq "blastx" and $db eq "allnucl"){ $execstring = "/home/groupii/ncbi-blast/bin/$prog -db \"" . ca +tfile(BLAST_DB_DIR, "allprot") . "\" -max_target_seqs 10 -word_size 5 + -evalue 100 -query \"$seqfile\""; } elsif ($prog eq "blastn") { $execstring = "/home/groupii/ncbi-blast/bin/$prog -db \"" . ca +tfile(BLAST_DB_DIR, $db) . "\" -max_target_seqs 10 -word_size 5 -pen +alty -3 -reward 2 -task blastn -evalue 100 -query \"$seqfile\""; } else { $execstring = "/home/groupii/ncbi-blast/bin/$prog -db \"" . ca +tfile(BLAST_DB_DIR, $db) . "\" -max_target_seqs 10 -word_size 5 -eval +ue 100 -query \"$seqfile\""; } print $cgi->header('text/plain'); print qx{$execstring}; } else { print $cgi->redirect('../blast.html'); } exit;
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Re: Software error...Plz help
by blue_cowdawg (Monsignor) on Jun 13, 2013 at 19:07 UTC | |
by hamzakhanvit (Initiate) on Jun 13, 2013 at 19:24 UTC | |
by Preceptor (Deacon) on Jun 13, 2013 at 21:42 UTC | |
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Re: Software error...Plz help
by runrig (Abbot) on Jun 13, 2013 at 19:58 UTC | |
by hamzakhanvit (Initiate) on Jun 13, 2013 at 22:02 UTC | |
by Anonymous Monk on Jun 14, 2013 at 07:18 UTC | |
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Re: Software error...Plz help
by Preceptor (Deacon) on Jun 13, 2013 at 17:54 UTC | |
by hamzakhanvit (Initiate) on Jun 13, 2013 at 18:17 UTC |