User:Lindenb/Notebook/InstitutThorax/2012/02/20

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Annovar changed annovar src to use curl (...) checkProgramUpdate ("wget"); for my $i (0 .. @urlin-1) { printerr "NOTICE: Downloading annotation database $urlin[$i] ... "; if ($verbose) { $sc = "curl --proxy xxxx.univ-nantes.prive:3128 -L -o $filein[$i] $urlin[$i]"; } else { $sc = "curl --proxy xxx.univ-nantes.prive:3128 -s -L -o $filein[$i] $urlin[$i]"; } if (system ($sc)) { #time-out is 10 seconds, with 1 retry attempt printerr "Failed\n"; $verbose and print "WARNING: unable to execute system command: <$sc>\n"; unlink ($filein[$i]); #delete the temporary files generated by wget $fail{$i}++; } else { printerr "OK\n"; $count_success++; } also commented out the check for updates. Need to free port for proxy: www.openbioinformatics.org and http://bioinform.med.usc.edu/annovar ./annotate_variation.pl -downdb -buildver hg19 gene humandb ./annotate_variation.pl -downdb -buildver hg19 knownGene humandb ./annotate_variation.pl -downdb -buildver hg19 wgEncodeGencodeManualV4 humandb also tfbs, mirna, mirnatarget, dgv, snp135 ./annotate_variation.pl -downdb gerp++elem -webfrom annovar -buildver hg19 humandb