gungorbudak / express

A database of ocular transcriptome expression profiling

Express

A database of transcriptome profiles encompassing known and novel transcripts across multiple developmental stages in eye tissues in mouse

Production server

Express is running on https://sysbio.sitehost.iu.edu/express/.

Local server

Requirements

After setting up an environment including Apache and MySQL servers, you will need following files and operations to set up the actual local server for Express.

1. This repository

    cd /path/to/www # actual root directory for Apache server
    git clone https://github.com/gungorbudak/express.git
   

2. Change the base URL at 4th line of assets/js/app.js into localhost

    perl -pi -e "s/sysbio\.sitehost\.iu\.edu\//localhost/g" path/to/www/express/assets/js/app.js
   

3. A directory called resources under root directory

    cd /path/to/www/express # actual root of the cloned repository
    mkdir resources
   

4. Custom GENCODE vM7 annotation and XML files under resources directory

    cd /path/to/www/express/resources
    wget https://sysbio.sitehost.iu.edu/express/resources/gencode.vM7.tgz
    tar -zxfv gencode.vM7.tgz
    rm gencode.vM7.tgz
   

5. 2bit format for Mus musculus 10 reference genome (from UCSC) under resources directory

    cd /path/to/www/express/resources
    wget http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit
   

6. The MySQL dump of Express database

    cd /path/to/www/express/resources
    wget https://sysbio.sitehost.iu.edu/express/resources/express.sql.gz
    gunzip < express.sql.gz | mysql -u user -p express
    rm express.sql.gz
   

After completing these steps, you should be able to see the local server for Express on http://localhost/express/.