Annovar And Ubuntu 12.10 - Database Download
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11.0 years ago
Achim • 0

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?

ubuntu annovar • 4.4k views
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Do you have the right perl modules installed, those that provide Net::FTP and/or LWP::UserAgent?

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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 ;)

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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?

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