User:Lindenb/Notebook/InstitutThorax/2012/02/20: Difference between revisions
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proxy problem: add to download http://www.openbioinformatics.org/annovar/download/hg19_refGeneMrna.fa.gz by hand, put it into the humandb dir | 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/ | |||
Revision as of 05:05, 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 -o $filein[$i] $urlin[$i]";
} else {
$sc = "curl --proxy xxx.univ-nantes.prive:3128 -s -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/
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