How to setup a BOLD data mirror yourself?

Dr. Di LiuInstitute of Microbiology, Chinese Academy of Sciences

@Informatics pre-conference workshop

What is BOLD Mirror?

• BOLD Mirror is data mirror of BOLD• It is a project of iBOL WG3.2• It is developed by the Institute of

Microbiology, Chinese Academy of Sciences• Everyone can setup BOLD mirror and use the

data locally• It will help the global distribution and the use

of BOLD data

What shall I do if I am interested in it?

• Visit our website: http://www.boldmirror.net

• Contact us:– Dr. Juncai Ma, ma@im.ac.cn– Dr. Di Liu, liud@im.ac.cn

The environments for installation

• Linux (we are using Ubuntu)• Apache• MySQL• PHP

Files within BOLDmirror v1.1

1. README.doc, README

2. boldmirror_web.zip: Files to create the web site

3. bold20111018.sql.gz: SQL files to create database

4. barcode-script.zip: Scripts for daily update.

5. logclient.zip: Scripts to collect the access logs

6. Software/, software you need to install beforehand, including Apache, MySQL, …

Installation

• Step 1. Create the database of boldmirror.– You can create the database with command or GUI

tool

• Then uncompress the SQL file, and run the sql file to create the tables and insert the data.

• It will take several minutes, please wait.

Installation• Step 2. Setup the WEB.

• Uncompress boldmirror_web.zip, and copy the boldmirror folder to your web server document root or create the link to the boldmirror by command – “sudo ln –s YOURBOLDMIRRORPATH

YOURWEBSERVERDOCUMENTROOT”.

• Make some configurations. – Modify file "boldmirror/system/application/config/database.php"

according to your database configuration.

http://Your_APACHE_URL/

Installation

• Step 3. Deploy the scripts for daily update – Uncompress barcode-script.zip– There are four folders in the barcode directory:

conf ,data ,logs and parsefiles. – Please modify the file “conf/barcode.conf”.

Installation

• Use crontab for daily update– “crontab –e”– “0 1 * * * cd YOURBARCODE_BASE_DIR/parsefiles

&& perl barcode.pl 2>&1”

THANKS

Contact us at anytime when you meet problem