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.
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This repository
cd /path/to/www # actual root directory for Apache server git clone https://github.com/gungorbudak/express.git
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Change the base URL at 4th line of
assets/js/app.js
into localhostperl -pi -e "s/sysbio\.sitehost\.iu\.edu\//localhost/g" path/to/www/express/assets/js/app.js
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A directory called
resources
under root directorycd /path/to/www/express # actual root of the cloned repository mkdir resources
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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
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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
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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/.