User:Lindenb/Notebook/InstitutThorax/2012/02/20: Difference between revisions
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printerr "NOTICE: Downloading annotation database $urlin[$i] ... "; | printerr "NOTICE: Downloading annotation database $urlin[$i] ... "; | ||
if ($verbose) { | if ($verbose) { | ||
$sc = "curl --proxy xxxx.univ-nantes.prive:3128 | $sc = "curl --proxy xxxx.univ-nantes.prive:3128 -L -o $filein[$i] $urlin[$i]"; | ||
} else { | } else { | ||
$sc = "curl --proxy xxx.univ-nantes.prive:3128 -s -o $filein[$i] $urlin[$i]"; | $sc = "curl --proxy xxx.univ-nantes.prive:3128 -s -L -o $filein[$i] $urlin[$i]"; | ||
} | } | ||
if (system ($sc)) { #time-out is 10 seconds, with 1 retry attempt | if (system ($sc)) { #time-out is 10 seconds, with 1 retry attempt | ||
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add to download http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.gz | add to download http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.gz | ||
later I asked an access for the proxy and www.openbioinformatics.org: | |||
Revision as of 08:15, 20 February 2012
 Project name
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<html><img src="/images/9/94/Report.png" border="0" /></html> Main project page |
Annovarchanged 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++;
}
./annotate_variation.pl -downdb -buildver hg19 gene humandb proxy problem: add to download http://www.openbioinformatics.org/annovar/download/hg19_refGeneMrna.fa.gz by hand, put it into the humandb dir scp hg19_refGeneMrna.fa.gz lindenb@xxxx.162:/data/users/lindenb/annovar/humandb/ and gunzip hg19_refGeneMrna.fa.gz
./annotate_variation.pl -downdb -buildver hg19 knownGene humandb other tracks: ./annotate_variation.pl -downdb -buildver hg19 wgEncodeGencodeManualV4 humandb ./annotate_variation.pl -downdb -buildver hg19 tfbs humandb .. and dgv, segdup, mirna, mirnatarget add to download http://www.openbioinformatics.org/annovar/download/hg19_gerp++elem.txt.gz later I asked an access for the proxy and www.openbioinformatics.org:
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