hfang-bristol / XGRm-site

XGRm - eXploring Genomic Relations (Model Organisms)

Source code for the XGRm web server

@ Overview

The XGRm web server offers real-time enrichment and subnetwork analyses for a user-input list of genes, SNPs, or genomic regions, through leveraging ontologies, networks, and many others (such as e/pQTL, promoter capture Hi-C, and enhancer-gene maps).

The web server provides users with a more integrated and user-friendly experience, featuring: ENRICHMENT ANALYSER (GENES) - EAG identifying enriched ontology terms from input gene list; ENRICHMENT ANALYSER (REGIONS) - EAR identifying enriched ontology terms for genes linked from input genomic region list; SUBNETWORK ANALYSER (GENES) - SAG identifying a gene subnetwork based on input gene-level summary data; and SUBNETWORK ANALYSER (REGIONS) - SAR identifying a gene subnetwork based on genes linked from input genomic region-level summary data.

To learn how to use the XGRm web server, a user manual has been made available here with step-by-step instructions.

@ Development

The XGRm web server was developed using Mojolicious and Bootstrap, supporting a mobile-first and responsive webserver across all major platform browsers.

The folder my_xgrm has a tree-like directory structure with three levels:

my_xgrm
├── lib
│   └── My_xgrm
│       └── Controller
├── public
│   ├── XGRmbooklet
│   │   ├── index_files
│   │   └── libs
│   ├── app
│   │   ├── ajex
│   │   ├── css
│   │   ├── examples
│   │   ├── img
│   │   └── js
│   ├── dep
│   │   ├── HighCharts
│   │   ├── Select2
│   │   ├── bootstrap
│   │   ├── bootstrapselect
│   │   ├── bootstraptoggle
│   │   ├── dataTables
│   │   ├── fontawesome
│   │   ├── jcloud
│   │   ├── jqcloud
│   │   ├── jquery
│   │   ├── tabber
│   │   └── typeahead
│   └── tmp
├── script
├── t
└── templates
    └── layouts

@ Installation

Assume you have a ROOT (sudo) privilege on Ubuntu

1. Install Mojolicious and other perl modules

sudo su
# here enter your password

curl -L cpanmin.us | perl - Mojolicious
perl -e "use Mojolicious::Plugin::PODRenderer"
perl -MCPAN -e "install Mojolicious::Plugin::PODRenderer"
perl -MCPAN -e "install DBI"
perl -MCPAN -e "install Mojo::DOM"
perl -MCPAN -e "install Mojo::Base"
perl -MCPAN -e "install LWP::Simple"
perl -MCPAN -e "install JSON::Parse"
perl -MCPAN -e "install local::lib"
perl -MCPAN -Mlocal::lib -e "install JSON::Parse"

2. Install R

sudo su
# here enter your password

# install R
wget http://www.stats.bris.ac.uk/R/src/base/R-4/R-4.3.1.tar.gz
tar xvfz R-4.3.1.tar.gz
cd ~/R-4.3.1
./configure
make
make check
make install
R # start R

3. Install pandoc

sudo su
# here enter your password

# install pandoc
wget https://github.com/jgm/pandoc/releases/download/3.1/pandoc-3.1-linux-amd64.tar.gz
tar xvzf pandoc-3.1-linux-amd64.tar.gz --strip-components 1 -C /usr/local/

# use pandoc to render R markdown
R
rmarkdown::pandoc_available()
Sys.setenv(RSTUDIO_PANDOC="/usr/local/bin")
rmarkdown::render(YOUR_RMD_FILE, bookdown::html_document2(number_sections=F, theme="readable", hightlight="default"))

@ Deployment

Assume you place my_xgrm under your home directory

cd ~/my_xgrm
systemctl stop apache2.service
morbo -l 'http://*:80/' script/my_xgrm

@ Contact

For any bug reports, please drop email.