Pull annotation data

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hg19

cd /srv/epgg/data/data/subtleKnife/seq
wget -b -q http://epgg-test.wustl.edu/installdata/hg19.gz http://epgg-test.wustl.edu/installdata/hg19.gz.tbi
cd /srv/epgg/data/data/subtleKnife/hg19
wget http://epgg-test.wustl.edu/installdata/hg19/refGene.gz
wget http://epgg-test.wustl.edu/installdata/hg19/refGene.gz.tbi
wget http://epgg-test.wustl.edu/installdata/hg19/xenoRefGene.gz
wget http://epgg-test.wustl.edu/installdata/hg19/xenoRefGene.gz.tbi
wget http://epgg-test.wustl.edu/installdata/hg19/gencodeV17.gz
wget http://epgg-test.wustl.edu/installdata/hg19/gencodeV17.gz.tbi
wget http://epgg-test.wustl.edu/installdata/hg19/rmsk_ensemble.gz
wget http://epgg-test.wustl.edu/installdata/hg19/rmsk_ensemble.gz.tbi
wget http://epgg-test.wustl.edu/installdata/hg19/rmsk_all.gz
wget http://epgg-test.wustl.edu/installdata/hg19/rmsk_all.gz.tbi
wget http://epgg-test.wustl.edu/installdata/hg19/cpgisland.gz
wget http://epgg-test.wustl.edu/installdata/hg19/cpgisland.gz.tbi
wget -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk.tgz
tar zxvf rmsk.tgz
wget -b -q http://epgg-test.wustl.edu/installdata/hg19/gc5Base.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/placentalphastCons46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/placentalphastCons46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/placentalphyloP46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/placentalphyloP46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/primatephastCons46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/primatephastCons46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/primatephyloP46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/primatephyloP46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/vertebratephastCons46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/vertebratephastCons46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/vertebratephyloP46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/vertebratephyloP46way.gz.tbi 
wget -b -q http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign100mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign24mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign36mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign40mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign50mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign75mer.bigWig 
  • manipulate in database
mysql> create database hg19;
cd /srv/epgg/data/data/browserLoad
wget http://epgg-test.wustl.edu/installdata/hg19/sql.tgz
tar zxvf sql.tgz 
rm sql.tgz
cd hg19/
cat load.sql |mysql -uxxx -pyyy --local-infile=1 hg19
cd /srv/epgg/data/subtleKnife/config/hg19
cat makeDb.sql ../sessionUtils.sql |mysql -uUSER -p hg19 --local-infile=1
mv publichub.json /srv/epgg/data/data/subtleKnife/hg19/config
  • Modify "publichub.json" to publish your own track sets

mm10

cd /srv/epgg/data/data/subtleKnife/mm10

wget -b -q http://epgg-test.wustl.edu/installdata/mm10/cpgIsland.gz \
http://epgg-test.wustl.edu/installdata/mm10/cpgIsland.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm10/gc5Base.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/phastCons.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/phastCons60wayEuarchontoGlire.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/phastCons60wayGlire.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/phastCons60wayPlacental.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/phyloP60way.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/phyloP60wayEuarchontoglire.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/phyloP60wayGlire.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/phyloP60wayPlacental.bigWig \
http://epgg-test.wustl.edu/installdata/mm10/refGene.gz \
http://epgg-test.wustl.edu/installdata/mm10/refGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm10/rmsk.tgz \
http://epgg-test.wustl.edu/installdata/mm10/xenoRefGene.gz \
http://epgg-test.wustl.edu/installdata/mm10/xenoRefGene.gz.tbi

wget http://epgg-test.wustl.edu/installdata/mm10/rmsk_all.gz
wget http://epgg-test.wustl.edu/installdata/mm10/rmsk_all.gz.tbi

tar zxvf rmsk.tgz

wget http://epgg-test.wustl.edu/installdata/mm10/sql.tgz
tar zxvf sql.tgz

cd mm10
cat load.sql |mysql -u ...
cd /srv/epgg/data/data/subtleKnife/seq
wget -b -q http://epgg-test.wustl.edu/installdata/mm10.gz http://epgg-test.wustl.edu/installdata/mm10.gz.tbi

hg38

cd /srv/epgg/data/data/subtleKnife/hg38

wget -b -q http://epgg-test.wustl.edu/installdata/hg38/gc5Base.bigWig \
http://epgg-test.wustl.edu/installdata/hg38/refGene.gz \
http://epgg-test.wustl.edu/installdata/hg38/refGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg38/xenoRefGene.gz \
http://epgg-test.wustl.edu/installdata/hg38/xenoRefGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg38/rmsk_all.gz \
http://epgg-test.wustl.edu/installdata/hg38/rmsk_all.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg38/rmsk_ensemble.gz \
http://epgg-test.wustl.edu/installdata/hg38/rmsk_ensemble.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg38/rmsk.gz \

tar zxvf rmsk.tgz

wget http://epgg-test.wustl.edu/installdata/hg38/sql.gz
gunzip sql.gz
cat sql |mysql -uxxx -p hg38
cd /srv/epgg/data/data/subtleKnife/seq
wget -b -q http://epgg-test.wustl.edu/installdata/hg38.gz http://epgg-test.wustl.edu/installdata/hg38.gz.tbi

rheMac3

cd /srv/epgg/data/data/subtleKnife/seq
wget -b -q http://epgg-test.wustl.edu/installdata/rheMac3.gz http://epgg-test.wustl.edu/installdata/rheMac3.gz.tbi
cd /srv/epgg/data/data/subtleKnife/rheMac3
wget -b -q http://epgg-test.wustl.edu/installdata/rheMac3/gc5Base.bigWig \
http://epgg-test.wustl.edu/installdata/rheMac3/refGene.gz \
http://epgg-test.wustl.edu/installdata/rheMac3/refGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/rheMac3/xenoRefGene.gz \
http://epgg-test.wustl.edu/installdata/rheMac3/xenoRefGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/rheMac3/rmsk.tgz
tar zxvf rmsk.tgz

wget http://epgg-test.wustl.edu/installdata/rheMac3/rmsk_all.gz
wget http://epgg-test.wustl.edu/installdata/rheMac3/rmsk_all.gz.tbi

wget http://epgg-test.wustl.edu/installdata/rheMac3/sql.tgz
tar zxvf sql.tgz
cd rheMac3
cat load.sql |mysql -u ...

macFas_BGI

cd /srv/epgg/data/data/subtleKnife/seq
wget -b -q http://epgg-test.wustl.edu/installdata/macFas_BGI.gz http://epgg-test.wustl.edu/installdata/macFas_BGI.gz.tbi
cd /srv/epgg/data/data/subtleKnife/macFas_BGI
wget -b -q http://epgg-test.wustl.edu/installdata/macFas_BGI/gc5Base.bigWig \
http://epgg-test.wustl.edu/installdata/macFas_BGI/gene.gz \
http://epgg-test.wustl.edu/installdata/macFas_BGI/gene.gz.tbi \
http://epgg-test.wustl.edu/installdata/macFas_BGI/rmsk.tgz \
http://epgg-test.wustl.edu/installdata/macFas_BGI/rmsk_ensemble.gz \
http://epgg-test.wustl.edu/installdata/macFas_BGI/rmsk_ensemble.gz.tbi
tar zxvf rmsk.tgz
wget http://epgg-test.wustl.edu/installdata/macFas_BGI/sql.tgz
tar zxvf sql.tgz
cd macFas_BGI
cat load.sql |mysql -u ...

mm9

cd /srv/epgg/data/data/subtleKnife/seq
wget -b -q http://epgg-test.wustl.edu/installdata/mm9.gz http://epgg-test.wustl.edu/installdata/mm9.gz.tbi

cd /srv/epgg/data/data/subtleKnife/mm9
wget -b -q http://epgg-test.wustl.edu/installdata/mm9/gc5Base.bigWig \
http://epgg-test.wustl.edu/installdata/mm9/cpgisland.gz \
http://epgg-test.wustl.edu/installdata/mm9/cpgisland.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/ensGene.gz \
http://epgg-test.wustl.edu/installdata/mm9/ensGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/euarchontogliresphastCons30way.gz \
http://epgg-test.wustl.edu/installdata/mm9/euarchontogliresphastCons30way.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/euarchontogliresphyloP30way.gz \
http://epgg-test.wustl.edu/installdata/mm9/euarchontogliresphyloP30way.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/placentalphastCons30way.gz \
http://epgg-test.wustl.edu/installdata/mm9/placentalphastCons30way.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/placentalphyloP30way.gz \
http://epgg-test.wustl.edu/installdata/mm9/placentalphyloP30way.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/refGene.gz \
http://epgg-test.wustl.edu/installdata/mm9/refGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/rmsk_ensemble.gz \
http://epgg-test.wustl.edu/installdata/mm9/rmsk_ensemble.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/vertebratephastCons30way.gz \
http://epgg-test.wustl.edu/installdata/mm9/vertebratephastCons30way.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/vertebratephyloP30way.gz \
http://epgg-test.wustl.edu/installdata/mm9/vertebratephyloP30way.gz.tbi \
http://epgg-test.wustl.edu/installdata/mm9/wgEncodeCrgMapabilityAlign36mer.bigWig \
http://epgg-test.wustl.edu/installdata/mm9/wgEncodeCrgMapabilityAlign40mer.bigWig \
http://epgg-test.wustl.edu/installdata/mm9/wgEncodeCrgMapabilityAlign50mer.bigWig \
http://epgg-test.wustl.edu/installdata/mm9/wgEncodeCrgMapabilityAlign75mer.bigWig \
http://epgg-test.wustl.edu/installdata/mm9/wgEncodeCrgMapabilityAlign100mer.bigWig \
http://epgg-test.wustl.edu/installdata/mm9/xenoRefGene.gz \
http://epgg-test.wustl.edu/installdata/mm9/xenoRefGene.gz.tbi

wget http://epgg-test.wustl.edu/installdata/mm9/rmsk_all.gz
wget http://epgg-test.wustl.edu/installdata/mm9/rmsk_all.gz.tbi

wget http://epgg-test.wustl.edu/installdata/mm9/rmsk.tgz
tar zxvf rmsk.tgz

wget http://epgg-test.wustl.edu/installdata/mm9/sql.gz
gunzip sql.gz
cat sql | mysql -uuname -ppp mm9

rn4

wget http://epgg-test.wustl.edu/installdata/rn4.gz
wget http://epgg-test.wustl.edu/installdata/rn4.gz.tbi
mv rn4.gz rn4.gz.tbi /srv/epgg/data/data/subtleKnife/seq/
wget http://epgg-test.wustl.edu/installdata/rn4/rmsk_all.gz
wget http://epgg-test.wustl.edu/installdata/rn4/rmsk_all.gz.tbi
wget http://epgg-test.wustl.edu/installdata/rn4/refGene.gz
wget http://epgg-test.wustl.edu/installdata/rn4/refGene.gz.tbi
wget http://epgg-test.wustl.edu/installdata/rn4/xenoRefGene.gz
wget http://epgg-test.wustl.edu/installdata/rn4/xenoRefGene.gz.tbi
wget http://epgg-test.wustl.edu/installdata/rn4/gc5Base.bigWig
wget http://epgg-test.wustl.edu/installdata/rn4/sql.gz
gunzip sql.gz
cat sql | mysql -uuname -p rn4

tair10

wget http://epgg-test.wustl.edu/installdata/tair10.gz
wget http://epgg-test.wustl.edu/installdata/tair10.gz.tbi
wget http://epgg-test.wustl.edu/installdata/tair10/gc5Base.bigWig
wget http://epgg-test.wustl.edu/installdata/tair10/repeat.gz
wget http://epgg-test.wustl.edu/installdata/tair10/repeat.gz.tbi
wget http://epgg-test.wustl.edu/installdata/tair10/tair10Gene.gz
wget http://epgg-test.wustl.edu/installdata/tair10/tair10Gene.gz.tbi