Question: Annovar And Ubuntu 12.10 - Database Download
0
gravatar for Achim
6.1 years ago by
Achim0
Achim0 wrote:

I have a problem downloading additional databases on two Ubuntu 12.10 machines. On all my other PCs it is working without a Problem.

Here is what I get:

user@host:~/annovar$ perl annotate_variation.pl -buildver hg19 -downdb refgene humandb/ WARNING: cannot retrieve remote files automatically (by 'wget' command or by standard Net::FTP/LWP::UserAgent Perl module). Please manually download the following file, uncompress the files to humandb directory, then add a hg19_ prefix to the file names. http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refLink.txt.gz http://www.openbioinformatics.org/annovar/download/hg19_refGeneMrna.fa.gz

user@host:~/annovar$ perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refgene humandb/ WARNING: cannot retrieve remote files automatically (by 'wget' command or by standard Net::FTP/LWP::UserAgent Perl module). Please manually download the following file, uncompress the files to humandb directory, then add a hg19_ prefix to the file names. http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refLink.txt.gz http://www.openbioinformatics.org/annovar/download/hg19_refGeneMrna.fa.gz

wget is installed and working normally. Any Ideas? Can someone confirm that it is working with 12.10 normally?

annovar ubuntu download • 2.5k views
ADD COMMENTlink modified 5.7 years ago • written 6.1 years ago by Achim0

Do you have the right perl modules installed, those that provide Net::FTP and/or LWP::UserAgent?

ADD REPLYlink written 6.1 years ago by fo3c420

I installed nothing special. I am new at the institute here an my collegues who work with annovar 12.04 say that they did nothing special. So I think this is waht is missing... I try to google it but would be happy if you have any hint what to install ;)

ADD REPLYlink written 6.1 years ago by Achim0

If sounds like you have made some non-standard installation. The script is actually telling you that not even wget is available (wget is standard in Debian based distroes, as far as I know).

What is the output of which wget?

ADD REPLYlink written 5.7 years ago by David Westergaard1.4k
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