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

From OpenWetWare

Jump to: navigation, search
Project name Main project page

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



Personal tools