Tuesday, March 13, 2012

Failed: Install and use VAT

tar -zxvf libbios-1.0.0.tar.gz
cd libbios-1.0.0
./configure --prefix=/home/app/VAT/out/libbios-1.0.0;make;make install

tar -zxvf gsl-1.15.tar.gz
cd gsl-1.15
./configure --prefix=/home/app/VAT/out/gsl-1.15;;make;make install


#cd gd-libgd
#./configure --prefix=/home/app/VAT/out/libgd

#blatSuite34
unzip blatSuite.34.zip -d /home/app/VAT/out/blatSuite-34

tar -zxvf libs3-2.0.tar.gz
cd libs3-2.0
make DESTDIR=/home/app/VAT/out/libs3 install

export CPPFLAGS="-I/home/app/VAT/out/gsl-1.15/include -I/home/app/VAT/out/libbios-1.0.0/include -I/home/app/VAT/out/libs3/include -ggdb"
export LDFLAGS="-L/home/app/VAT/out/gsl-1.15/lib -L/home/app/VAT/out/libbios-1.0.0/lib -L/home/app/VAT/out/libs3/lib"

tar -zxvf vat-2.0.0.tar.gz
cd vat-2.0.0

#vim default.vatrc
#TABIX_DIR /home/app/tabix
#VAT_EXEC_DIR /home/app/VAT/out/vat/bin

./configure --prefix=/home/app/VAT/out/vat;make;make install
export VAT_CONFIG_FILE=/home/app/.vatrc



cd /home/app/test
gunzip gencode.v11.annotation.gtf.gz
awk '/\t(HAVANA|ENSEMBL)\tCDS\t/ {print}' gencode.v11.annotation.gtf | grep 'gene_type "protein_coding"' | grep 'transcript_type "protein_coding"' > gencode.v11.annotation.cds.gtpc.ttpc.gtf
/home/app/VAT/out/vat/bin/gencode2interval < gencode.v11.annotation.cds.gtpc.ttpc.gtf > gencode.v11.annotation.cds.gtpc.ttpc.interval


./faToTwoBit -noMask /tomato/data/hg19.fasta hg19.2bit

export LD_LIBRARY_PATH=/home/app/VAT/out/libbios-1.0.0/lib:/home/app/VAT/out/libs3/lib:/home/app/VAT/out/gsl-1.15/lib



/home/app/VAT/out/vat/bin/interval2sequences hg19.2bit gencode.v11.annotation.cds.gtpc.ttpc.interval exonic > gencode.v11.annotation.cds.gtpc.ttpc.exonic.fasta
#twoBitReadSeqFrag in chr6 start (53371710) >= end (53371710)
#Segmentation fault

/home/app/VAT/out/vat/bin/interval2sequences hg19.2bit gencode.v11.annotation.cds.gtpc.ttpc.interval genomic> gencode.v11.annotation.cds.gtpc.ttpc.genomic.fasta
#pass

/home/app/VAT/out/vat/bin/snpMapper gencode.v11.annotation.cds.gtpc.ttpc.interval gencode.v11.annotation.cds.gtpc.ttpc.genomic.fasta 1
#Segmentation fault

/home/app/VAT/out/vat/bin/indelMapper gencode.v11.annotation.cds.gtpc.ttpc.interval gencode.v11.annotation.cds.gtpc.ttpc.genomic.fasta 2

1 comment:

  1. Hi,

    I am facing the same issue too.
    Did you manage to fix this issue ?

    Best regards,
    Ambily

    ReplyDelete