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/ | scp hg19_refGeneMrna.fa.gz lindenb@xxxx.162:/data/users/lindenb/annovar/humandb/ | ||
and | |||
gunzip hg19_refGeneMrna.fa.gz | |||
same for knownGenes: | |||
./annotate_variation.pl -downdb -buildver hg19 knownGene humandb | |||
ENCODE tracks: | |||
./annotate_variation.pl -downdb -buildver hg19 wgEncodeGencodeManualV4 humandb | |||
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### --> | <!-- ##### DO NOT edit below this line unless you know what you are doing. ##### --> |
Revision as of 05:11, 20 February 2012
Project name | <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/ and gunzip hg19_refGeneMrna.fa.gz
./annotate_variation.pl -downdb -buildver hg19 knownGene humandb ENCODE tracks: ./annotate_variation.pl -downdb -buildver hg19 wgEncodeGencodeManualV4 humandb |