Menu ▾ ▴

Installation

Keith Ching

Installation

Currently, the installation procedure occurs through the SVN repository checkout. The files for CNV images are quite large, so it is not recommended to checkout the whole repository at once. Separate downloadable tarballs will be created once all the files in the repository have stabilized.

AWS instance installation.
~10 GB root

make sure to add nofail to /etc/fstab volumes otherwise you will be unable to get a shell on AWS if any disk fails to mount at startup.

#
LABEL=/     /           ext4    defaults,noatime  1   1
tmpfs       /dev/shm    tmpfs   defaults        0   0
devpts      /dev/pts    devpts  gid=5,mode=620  0   0
sysfs       /sys        sysfs   defaults        0   0
proc        /proc       proc    defaults        0   0
/dev/xvdf1  none    swap    sw      0       0
/dev/xvdg1  /disk1       ext4    defaults,nofail        0   2
/dev/xvdh1  /disk2       ext4    defaults,nofail        0   2
/dev/xvdi1  /disk3       ext4    defaults,nofail        0   2

Install prerequisites:

sudo yum update -y
sudo yum groupinstall -y "Web Server" "Perl Support"
sudo yum install svn
sudo yum groupinstall -y "Web Servlet Engine" "MySQL Database" "Development tools"
sudo yum install R-core.x86_64
sudo yum install R-core-devel.x86_64
sudo yum install libxml2-devel.x86_64

Modify Apache
sudo vi /etc/httpd/conf/httpd.conf

add FollowSymLinks to cgi-bin

<Directory "/var/www/cgi-bin">
    AllowOverride None
    Options FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

increase timeout limit to 600

# Timeout: The number of seconds before receives and sends time out.
#
Timeout 600

On OSX, add the Timeout parameter to /etc/apache2/httpd.conf

Start Apache

sudo service httpd start
#set to automatically run on startup
sudo chkconfig httpd on
chkconfig --list httpd

on OSX

sudo /usr/sbin/apachectl restart

Set up web
checkout the repository into a web folder

sudo svn checkout svn://svn.code.sf.net/p/cellx/code/web web

change permissions

sudo chown -R ec2-user web
sudo chgrp -R apache web
sudo chmod -R 775 web

create symbolic links.

cd /var/www/html
# make a tmp dir here
sudo mkdir tmp
sudo chmod 777 tmp/
# symbolic link where you installed the web repository to RPPA
sudo ln -s /disk1/web/var/www/html/RPPA/ RPPA
cd RPPA
sudo ln -s /disk1/web/var/www/cgi-bin/RPPA/rlib/ rlib

cd /var/www/cgi-bin/
sudo ln -s /disk1/web/var/www/cgi-bin/RPPA/ RPPA

Configure Perl

sudo cpan
install Statistics::Descriptive
install Data::Table

Config CELLX

cd /var/www/cgi-bin/RPPA/lib/
sudo vi cellx_config.pl

Config mysql

#start mysql
sudo service mysqld start
sudo chkconfig mysqld on
#set root
sudo mysqladmin -u root password NEWPASSWORD

# login to mysql
mysql> create database cellx;
Query OK, 1 row affected (0.00 sec)
mysql> CREATE USER 'cellx'@'localhost' IDENTIFIED BY 'mypassword';
Query OK, 0 rows affected (0.00 sec)
# read only user
mysql> GRANT SELECT ON cellx.* TO 'cellx'@'localhost';
Query OK, 0 rows affected (0.00 sec)
mysql> flush privileges;
Query OK, 0 rows affected (0.00 sec)

Loading the database
Database restoration typically uses sql dumps from the mysqldump utility. However, this method has proven impractical for AWS RDS because the time takes days, incurs hundreds of millions of transaction costs, and often chokes when it gets to the expression table.

Consequently I had created table dumps and a loader script to load directly from a local file. This has the effect of loading faster until it chokes on the expression table.

My conclusion is that the AWS RDS service cannot be effectively utilized for CELLX. Instead, I have provided the pre-indexed MyISAM tables that one merely needs to copy into the correct location and the database is immediately ready for queries.

#expand mysql tar (~45 GB space needed)
obtain the database tarball from the files download section of sourceforge.

#shutdown mysqld
sudo service mysqld stop
# remove the old db
cd /var/lib/mysql/
sudo rm -rf cellx/

#symbolic link cellx database, or copy files
sudo tar zxvf /disk1/database/cellx.tar.gz

# change permissions to mysql
sudo chown -R mysql cellx/
sudo chgrp -R mysql cellx/
sudo chmod -R 755 cellx/
sudo ln -s /disk2/cellx/ cellx

#restart mysqld
sudo service mysqld start

Tomcat

# checkout the Rserve code
sudo svn checkout svn://svn.code.sf.net/p/cellx/code/src src

# copy libraries
sudo cp src/rserve/lib/*.jar /usr/share/tomcat6/lib/
# copy web app
sudo cp src/rserve/Rserver/deploy/Rserver.war /usr/share/tomcat6/webapps/

# start tomcat
sudo service tomcat6 start
sudo chkconfig --level 345 tomcat6 on

Install Rserve

sudo R CMD INSTALL src/rserve/Rserve_0.5-3.tar.gz
# edit src/rserve/Rserver/etc/rserve.config
sudo cp src/rserve/Rserver/etc/rserve.config /etc/

# install R libraries
sudo R
# at R prompt
source("http://bioconductor.org/biocLite.R")
biocLite('gplots')
biocLite('genefilter')
biocLite("mixtools")
# start R serve
cd src/rserve
sudo R CMD Rserve --RS-conf Rserv.conf

Related

Wiki: Home