We assume you will install most bioinformatics tools in folder /public/programs/. Also, we assume you will install the system in folder /var/www/html/chomics/ and your system will have URL like this: http:/my.domain.name/chomics/. If your installation is different, please update your system settings accordingly.
The system is tested and developed on CentOS, 64bit, v7. Other Linux system may also work. After installing CentOS (minimal installation), please make sure to install "Development Tools" and some basic commands. You also need to install AMP (Apache, Mariadb, and PHP) and configure them correctly. We assume your web is in folder /var/www/html/ and apache user/group are apache/apache. In addition, you may need to turn off firewall and SELINUX. Please visit your website first to verify. Here are the suggested commands:
# Install development tools sudo yum -y install wget unzip bzip2 sudo yum -y group install "Development Tools" sudo yum -y install man-pages man-db man # Or, try with this command: sudo yum groupinstall "Development Tools" # Stop firewalld systemctl stop firewalld # Disable firewalld systemctl disable firewalld # Status of firewalld systemctl status firewalld # temporarily disable SELinux sudo setenforce 0 # Permanently disable SELinux, edit file and change to "SELINUX=disabled" sudo vi /etc/selinux/config # Save the file and reboot your CentOS system sudo shutdown -r now sudo sestatus # Install MariaDB sudo yum -y install mariadb-server # Allow remote access, only necessary if filewall is running firewall-cmd --zone=public --add-service=mysql --permanent # Set the root password /usr/bin/mysql_secure_installation # Make sure to launch mariadb at reboot sudo systemctl enable mariadb.service # Start and stop the database service sudo systemctl start mariadb.service # Installing Apache sudo yum -y install httpd sudo systemctl start httpd.service sudo systemctl enable httpd.service # If you still have filewall running sudo firewall-cmd --permanent --zone=public --add-service=http sudo firewall-cmd --permanent --zone=public --add-service=https sudo firewall-cmd --reload # Install PHP sudo yum-config-manager --enable remi-php72 sudo yum -y install php php-opcache # Getting MySQL Support In PHP sudo yum -y install php-mysqlnd php-pdo sudo yum -y install php-gd php-ldap php-odbc php-pear php-xml php-xmlrpc php-mbstring php-soap curl curl-devel # Install phpMyAdmin sudo yum -y install phpMyAdmin # Update phpMyAdmin settings, if necessary sudo vi /etc/httpd/conf.d/phpMyAdmin.conf # Update apache settings, if necessary sudo vi /etc/httpd/conf/httpd.conf # Restart Apache Server sudo systemctl restart httpd.service
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip unzip fastqc_v0.11.5.zip mv FastQC /public/programs/fastqc/fastqc_v0.11.5 ln -s /public/programs/fastqc/fastqc_v0.11.5 /public/programs/fastqc/latest chmod 775 -R /public/programs/fastqc/*
wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2 wget https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2 wget https://github.com/samtools/htslib/releases/download/1.8/htslib-1.8.tar.bz2 bzip2 -d bcftools-1.8.tar.bz2 bzip2 -d htslib-1.8.tar.bz2 bzip2 -d samtools-1.8.tar.bz2 tar xf bcftools-1.8.tar tar xf htslib-1.8.tar tar xf samtools-1.8.tar cd samtools-1.8/ ./configure --prefix=/usr/local make sudo make install cd ../htslib-1.8/ ./configure --prefix=/usr/local make sudo make install cd ../bcftools-1.8/ ./configure --prefix=/usr/local make sudo make install
wget http://downloads.sourceforge.net/project/subread/subread-1.5.0-p1/subread-1.5.0-p1-Linux-x86_64.tar.gz sudo mkdir /public/programs/subread sudo mv subread-1.5.0-p1-Linux-x86_64.tar.gz /public/programs/subread cd /public/programs/subread sudo tar zxvf subread-1.5.0-p1-Linux-x86_64.tar.gz subread-1.5.0-p1-Linux-x86_64 sudo mkdir latest sudo cp -r subread-1.5.0-p1-Linux-x86_64/* latest/
wget https://github.com/erickramer/GSEAR/archive/master.zip unzip master.zip mv GSEAR-master/src/gsea /public/programs/gsea
cd /public/programs/ mkdir homer cd homer wget http://homer.salk.edu/homer/configureHomer.pl perl ./configureHomer.pl -install perl ./configureHomer.pl -install mm10 perl ./configureHomer.pl -list perl ./configureHomer.pl -update chmod -R 775 *
sudo R
source("http://bioconductor.org/biocLite.R");
biocLite( c("Rsubread","limma","edgeR","PGSEA","made4","XML","annotate","genefilter","openssl", "httr","stringr","reshpage","piano","optparse","pathview","data.table","impute", "combinat", "explor","missMDA","KEGGgraph","KEGGREST","pathview","FactoMineR","org.Mm.eg.db"));
q();
wget https://cran.r-project.org/src/contrib/Archive/MetaDE/MetaDE_1.0.5.tar.gz
sudo R CMD INSTALL MetaDE_1.0.5.tar.gz
sudo R
#remove old version first,
remove.packages("BiocInstaller") ;
#RankProd requires latest bioconductor installer
source("https://bioconductor.org/biocLite.R"); #if error occurs, re-start R
biocLite("RankProd");
#make sure the version installed is RankProd_3.4.0 or later
library("Rsubread");
library("limma");
library("edgeR");
library("PGSEA");
library("made4");
library("stringr");
library("piano");
library("optparse");
library("data.table");
library("explor");
library("missMDA");
library("GO.db");
library("AnnotationDbi");
library("stats4");
library("BiocGenerics");
library("parallel");
library("BiocGenerics");
library("Biobase");
library("S4Vectors");
library("KEGG.db");
library("annaffy");
library("ade4");
library("RColorBrewer");
library("gplots");
library("scatterplot3d");
library("genefilter");
library("pathview");
library("help=pathview");
library("MetaDE");
library("FactoMineR");
Please download the system package (file name: chomics.tar.gz) from the URL we send to you in the e-mail. Then use the following commands to install:
tar xzvf chomics.tar.gz mv chomics /var/www/html/.
The initial database contents are in file /var/www/html/chomics/bxaf_setup/config.sql.gz
# Start the MariaDB shell /usr/bin/mysql -u root -p # Create database and set up user permissions CREATE USER 'chomics'@'localhost' IDENTIFIED BY 'CHOMICS@2020'; CREATE DATABASE IF NOT EXISTS `chomics`; GRANT ALL PRIVILEGES ON `chomics`.* TO 'chomics'@'localhost'; FLUSH PRIVILEGES; zcat /var/www/html/chomics/bxaf_setup/chomics.sql.gz | /usr/bin/mysql -u root -p chomics
Notice that, we have a symbolic link in folder /var/www/html/chomics/app_data/files_core/PICR. This folder container CHO genome information, which is over 5GB. If you don't have this package, please delete this symbolic link, download the compressed package, uncompress and move it in this folder.
rm -rf /var/www/html/chomics/app_data/files_core/gsea wget http://chomics.com/gsea.tar.gz tar xzvf gsea.tar.gz mv gsea /var/www/html/chomics/app_data/files_core/. rm -rf /var/www/html/chomics/app_data/files_core/PICR wget http://chomics.com/PICR.tar.gz tar xzvf PICR.tar.gz mv PICR /var/www/html/chomics/app_data/files_core/.
Please review and update /var/www/html/chomics/bxaf_setup/config.sql according to your server settings. Also, update file ownership and permissions.
sudo chown apache:apache -R /var/www/html/chomics/ sudo chmod 775 -R /var/www/html/chomics/
Please open a browser (Firefox) and visit http:/my.domain.name/chomics/ to test the system.