WashU_install

pip install SOAPpy
sudo service mysqld start
sudo yum install libpng ghostscript GMT hdf5
sudo yum install zlib-devel ncurses-devel
sudo yum install openssl-devel
sudo yum install openssl-devel
sudo yum install curl-devel
sudo yum install libssh2-devel
sudo yum install librsvg2-devel
tar -xf /home/train/software/libpng-1.2.59.tar.xz -C /home/train/
cd
cd libpng-1.2.59/
mkdir /opt/sysoft/libpng12
./configure --prefix=/opt/sysoft/libpng12/
make -j 8
make install
echo 'export LD_LIBRARY_PATH=/opt/sysoft/libpng12/lib/:$LD_LIBRARY_PATH' >> ~/.bashrc.WashU
echo 'export C_INCLUDE_PATH=/opt/sysoft/libpng12/include/:$C_INCLUDE_PATH' >> ~/.bashrc.WashU
source ~/.bashrc.WashU
sudo vim /etc/httpd/conf/httpd.conf
<IfModule mpm_worker_module>
   LoadModule cgid_module modules/mod_cgid.so
</IfModule>
<IfModule mpm_event_module>
   LoadModule cgid_module modules/mod_cgid.so
</IfModule>
<IfModule mpm_prefork_module>
   LoadModule cgi_module modules/mod_cgi.so
</IfModule>
sudo service httpd start
cd
rm -rf libpng-1.2.59/
mkdir WashU
cd WashU/
git clone https://github.com/epgg/eg.git

#Compile the cgi-bin program
cd eg/cgi-bin/jsmn-example/
sudo vim /etc/httpd/conf/httpd.conf
LoadModule cgid_module modules/mod_cgid.so
Options FollowSymLinks ExecCGI
AddHandler cgi-script .cgi

sudo yum install jsoncpp-devel
scp root@192.168.199.220:/root/Downloads/curl-7.61.1.tar.gz /home/train/software/
tar -zxf /home/train/software/curl-7.61.1.tar.gz -C /home/train/
cd /home/train/curl-7.61.1/
mkdir /opt/sysoft/curl-7.61.1
./configure --prefix=/opt/sysoft/curl-7.61.1/
make -j 8
make test
make install
echo 'export LD_LIBRARY_PATH=/opt/sysoft/curl-7.61.1/lib/:$LD_LIBRARY_PATH' >> ~/.bashrc.WashU
echo 'export C_INCLUDE_PATH=/opt/sysoft/curl-7.61.1/include/:$C_INCLUDE_PATH' >> ~/.bashrc.WashU
echo 'export PATH=/opt/sysoft/curl-7.61.1/bin/:$PATH' >> ~/.bashrc.WashU
source ~/.bashrc.WashU
cd ..
rm -rf curl-7.61.1/
cd /home/train/WashU/eg/cgi-bin/jsmn-example
make
cd ../jsmn/
make 
cd ..
cp subtleKnife.c subtleKnife.c.bak
vim subtleKnife.c
#define WWWT "/var/www/html/browser/t" // Docker version
#define BINdir "."
#define Mysqlserver "localhost" // Deployment version
#define Mysqlserver "localhost" // Docker version
#define Mysqluser "hguser"
#define Mysqlpswd "hguser"
cp postdeposit.c postdeposit.c.bak
vim postdeposit.c
#define WWWT "/var/www/html/browser/t" // Docker version
make 
sudo cp postdeposit subtleKnife /var/www/cgi-bin/
sudo cp ucsc2jsonhub.py /var/www/cgi-bin/

#Directories
sudo mkdir -p /var/www/html/browser/t
sudo mkdir /srv/epgg
sudo chown apache.apache /srv/epgg/
sudo mkdir /srv/epgg/data
cd /srv/epgg/data/
sudo mkdir data
cd data/
sudo mkdir subtleKnife
cd subtleKnife/
sudo mkdir seq
sudo mkdir /srv/epgg/data/data/subtleKnife/hg19
sudo mkdir /srv/epgg/data/data/subtleKnife/hg19/config
sudo mkdir /srv/epgg/data/data/subtleKnife/hg19/session
sudo mkdir /srv/epgg/data/trash
sudo chown apache.apache /srv/epgg/data/trash/
sudo ln -s /srv/epgg/data/trash /usr/lib

cd ~/WashU/eg/
cd browser/
sudo mv css/ index.html js/ images/ /var/www/html/browser/
cd ..
sudo mv config/treeoflife /srv/epgg/data/data/subtleKnife/
sudo cp config/hg19/tracks.json /srv/epgg/data/data/subtleKnife/hg19/config/
sudo cp config/hg19/publichub.json /srv/epgg/data/data/subtleKnife/hg19/config/
cd /srv/epgg/data/data/subtleKnife/hg19/
sudo vim hg19_download.sh
####################################
wget -c http://egg.wustl.edu/d/hg19/refGene.gz
wget -c http://egg.wustl.edu/d/hg19/refGene.gz.tbi
wget -c http://egg.wustl.edu/d/hg19/gencodeV17.gz
wget -c http://egg.wustl.edu/d/hg19/gencodeV17.gz.tbi
wget -c http://egg.wustl.edu/d/hg19/xenoRefGene.gz
wget -c http://egg.wustl.edu/d/hg19/xenoRefGene.gz.tbi
####################################
sudo bash hg19_download.sh
sudo rm hg19_download.sh

mysql -u root -p123456
mysql> GRANT ALL ON *.* TO 'hguser'@'localhost' IDENTIFIED BY 'hguser' WITH GRANT OPTION;
mysql> FLUSH PRIVILEGES;
mysql> CREATE DATABASE hg19;
mysql> FLUSH PRIVILEGES;
mysql> QUIT
cd ~/WashU/eg/config/
cat sessionUtils.sql | mysql -u hguser -p hg19
cd hg19
cat makeDb.sql | mysql -u hguser -p hg19
sudo vim /etc/httpd/conf/httpd.conf
#############################
<Location /var/www/cgi-bin>
Header set Access-Control-Allow-Origin "*"
</Location>
#############################
sudo service httpd restart
sudo service mysqld restart

cd /srv/epgg/data/data/subtleKnife/seq/
sudo wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19.gz http://epgg-test.wustl.edu/installdata/hg19.gz.tbi

cd
mkdir -p ~/WashU/webdata/hg19
cd ~/WashU/webdata/hg19/
vim download.sh
##########################################################
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk_ensemble.gz
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk_ensemble.gz.tbi
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk_all.gz
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk_all.gz.tbi
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/cpgisland.gz
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/cpgisland.gz.tbi

wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk.tgz

wget -c -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 -c -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
##########################################################################################
tar zxvf rmsk.tgz
sudo ln -sv /home/train/WashU/webdata/hg19/* /srv/epgg/data/data/subtleKnife/hg19/
cd /srv/epgg/data/data/subtleKnife/
sudo wget http://epgg-test.wustl.edu/installdata/hg19/sql.tgz
sudo tar -zxf sql.tgz 
sudo rm sql.tgz
cd hg19/
cat load.sql | mysql -u hguser -p hg19
cd ~/WashU/eg/config/hg19/
cat makeDb.sql ../sessionUtils.sql | mysql -u hguser -p hg19

cd /srv/epgg/data/data/subtleKnife/
sudo mkdir hg38
cd hg38/
sudo vim download.sh
#######################################
wget -c -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 \
#######################################
cd
cd WashU/webdata/
mkdir hg38
cd hg38
sudo mv /srv/epgg/data/data/subtleKnife/hg38/download.sh /home/train/WashU/webdata/hg38/
bash download.sh
wget -c https://epgg-test.wustl.edu/installdata/hg38/rmsk_ensemble.gz.tbi
wget -c https://epgg-test.wustl.edu/installdata/hg38/rmsk.tgz
tar -zxf rmsk.tgz
cd /srv/epgg/data/data/subtleKnife/hg38/
sudo mkdir config
sudo mkdir session
sudo chown apache.apache /srv/epgg/data/data/subtleKnife/hg38/session/
sudo cp ../hg19/config/publichub.json config/
sudo ln -sv /home/train/WashU/webdata/hg38/* /srv/epgg/data/data/subtleKnife/hg38/
sudo wget http://epgg-test.wustl.edu/installdata/hg38/sql.gz
sudo gunzip sql.gz
sudo mysql -u root -p123456
mysql> CREATE DATABASE hg38;
mysql> FLUSH PRIVILEGES;
mysql> quit
cat sql | mysql -u hguser -p hg38
cd ../seq/
sudo wget -c -b -q http://epgg-test.wustl.edu/installdata/hg38.gz http://epgg-test.wustl.edu/installdata/hg38.gz.tbi

cd
cd software/
wget http://hgdownload.soe.ucsc.edu/admin/jksrc.zip
cp jksrc.zip /home/train/
unzip jksrc.zip -d /opt/sysoft/
cd /opt/sysoft/kent/src/
export MACHTYPE="x86_64"
export USE_SSL=1
sudo yum install uuid-devel.x86_64
sudo yum install uuid-c++-devel.x86_64
sudo yum install libuuid-devel
make libs
mkdir utils/bwquery
cd utils/bwquery/
cp ~/WashU/eg/cgi-bin/bwquery/* .
make 
sudo ln -sv /opt/sysoft/kent/src/utils/bwquery/ /var/www/cgi-bin/
/var/www/cgi-bin/bwquery/bwquery https://vizhub.wustl.edu/hubSample/hg19/sample.bigWig chr7 27053199 27373567 20 /opt/sysoft/kent/src/utils/bwquery/bwOutput.txt 1
sudo cp bwOutput.txt /srv/epgg/data/data/subtleKnife/hg19/

cd /srv/epgg/data
sudo tar -xf /home/train/software/samtools-0.1.19.tar.bz2 -C /srv/epgg/data/
cd samtools-0.1.19/
sudo make 
sudo ln -sv /srv/epgg/data/samtools-0.1.19/samtools /usr/local/bin/
cd /opt/sysoft/
mkdir -p subtleKnife/scripts/bamliquidator
cd subtleKnife/scripts/bamliquidator/
wget -c https://egg.wustl.edu/script/bamliquidator/bamliquidator.c
wget https://egg.wustl.edu/script/bamliquidator/bamliquidator.o
wget https://egg.wustl.edu/script/bamliquidator/make.sh
chmod 755 make.sh 
sudo ./make.sh 
cp bamliquidator /usr/local/bin/
sudo yum install sendmail-devel

cd /srv/epgg/data/
sudo tar -xf /home/train/software/tabix-0.2.6.tar.bz2 -C /srv/epgg/data/
cd tabix-0.2.6/
sudo make 
sudo ln -sv /srv/epgg/data/tabix-0.2.6/tabix /usr/local/bin/
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