Friday, June 17, 2011

VAT

VAT

http://archive.gersteinlab.org/proj/VAT/


$pwd
$HOME/VAT

#download&install GNU Scientific Library
$wget http://mirror.clarkson.edu/gnu/gsl/gsl-1.15.tar.gz
$sudo tar -zxvf gsl-1.15.tar.gz;cd gsl-1.15; ./configure; make; make install

#download&install gettext
$wget http://ftp.gnu.org/pub/gnu/gettext/gettext-0.18.1.1.tar.gz
$sudo tar -zxvf gettext-0.18.1.1.tar.gz;cd gettext-0.18.1.1;./configure; make; make install

#download GD Library
http://google-desktop-for-linux-mirror.googlecode.com/files/gd-2.0.35.tar.gz
sudo tar -zxvf gd-2.0.35.tar.gz;cd gd/2.0.35/;./configure; make; make install


#libbios
$wget http://homes.gersteinlab.org/people/lh372/VAT/libbios-1.0.0.tar.gz
$sudo tar -zxvf libbios-1.0.0.tar.gz; cd libbios-1.0.0
$sudo export CPPFLAGS="-I$HOME/VAT/libbios-1.0.0/include"
$sudo export LDFLAGS="-L$HOME/VAT/libbios-1.0.0/lib"
$sudo ./configure;make;make install


#twoBitToFa is required for "interval2sequences"
$wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa
$chmod +x twoBitToFa
$cp twoBitToFa $HOME/tool/


#download&install VAT package
$wget http://homes.gersteinlab.org/people/lh372/VAT/vat-1.0.0.tar.gz
$tar -zxvf vat-1.0.0.tar.gz; cd vat-1.0.0
$mkdir tmp
$./configure --prefix=$HOME/VAT/vat-1.0.0/tmp;make;make install
$mv tmp/* $HOME/VAT/tool


wget ftp://ftp.sanger.ac.uk/pub/gencode/release_3c/gencode.v3c.annotation.GRCh37.gtf.gz
gunzip gencode.v3c.annotation.GRCh37.gtf.gz


wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

export LD_LIBRARY_PATH=$HOME/VAT/lib:$LD_LIBRARY_PATH

cat x2.snp.vcf | snpMapper gencode.v3c.annotation.GRCh37.cds.gtpc.ttpc.interval gencode.v3c.annotation.GRCh37.cds.gtpc.ttpc.fa > x2.snp.annotated.vcf

cat x2.indel.vcf | indelMapper gencode.v3c.annotation.GRCh37.cds.gtpc.ttpc.interval gencode.v3c.annotation.GRCh37.cds.gtpc.ttpc.fa > x2.indel.annotated.vcf

2 comments:

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  2. Hello, are these instructions still valid? The FunSeq documentation points here for directions on how to install VAT as a prerequisite for FunSeq, but the current VAT documentation refers to VAT (v2.0.1) as a cloud application rather than a local one, so I'm sure what to do - install VAT v1 locally or VAT v2 and set it up to run locally instead of on Amazon? Thanks.
    --Lee

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